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Chiang BJ, Lin KY, Chen YF, Huang CY, Goh FJ, Huang LT, Chen LH, Wu CH. Development of a tightly regulated copper-inducible transient gene expression system in Nicotiana benthamiana incorporating a suicide exon and Cre recombinase. THE NEW PHYTOLOGIST 2024; 244:318-331. [PMID: 39081031 DOI: 10.1111/nph.20021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 07/15/2024] [Indexed: 09/17/2024]
Abstract
Chemical-inducible gene expression systems are commonly used to regulate gene expression for functional genomics in various plant species. However, a convenient system that can tightly regulate transgene expression in Nicotiana benthamiana is still lacking. In this study, we developed a tightly regulated copper-inducible system that can control transgene expression and conduct cell death assays in N. benthamiana. We tested several chemical-inducible systems using Agrobacterium-mediated transient expression and found that the copper-inducible system exhibited the least concerns regarding leakiness in N. benthamiana. Although the copper-inducible system can control the expression of some tested reporters, it is not sufficiently tight to regulate certain tested hypersensitive cell death responses. Using the MoClo-based synthetic biology approach, we incorporated the suicide exon HyP5SM/OsL5 and Cre/LoxP as additional regulatory elements to enhance the tightness of the regulation. This new design allowed us to tightly control the hypersensitive cell death induced by several tested leucine-rich repeat-containing proteins and their matching avirulence factors, and it can be easily applied to regulate the expression of other transgenes in transient expression assays. Our findings offer new approaches for both fundamental and translational studies in plant functional genomics.
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Affiliation(s)
- Bing-Jen Chiang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115 201, Taiwan
| | - Kuan-Yu Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115 201, Taiwan
| | - Yi-Feng Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115 201, Taiwan
| | - Ching-Yi Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115 201, Taiwan
| | - Foong-Jing Goh
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115 201, Taiwan
| | - Lo-Ting Huang
- Department of Plant Pathology, National Chung Hsing University, Taichung, 402 202, Taiwan
| | - Li-Hung Chen
- Department of Plant Pathology, National Chung Hsing University, Taichung, 402 202, Taiwan
- Advanced Plant and Food Crop Biotechnology Center, National Chung Hsing University, Taichung, 402 202, Taiwan
| | - Chih-Hang Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115 201, Taiwan
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2
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Guiziou S. Biocomputing in plants, from proof of concept to application. Curr Opin Biotechnol 2024; 87:103146. [PMID: 38781700 DOI: 10.1016/j.copbio.2024.103146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/30/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024]
Abstract
In response to the challenges of climate change and the transition toward sustainability, synthetic biology offers innovative solutions. Most current plant synthetic biology applications rely on the constitutive expression of enzymes and regulators. To engineer plant phenotypes tuneable to environmental conditions and plant cellular states, the integration of multiple signals in synthetic circuits is required. While most circuits are developed in model organisms, numerous tools were recently developed to implement biocomputation in plant synthetic circuits. I presented in this review the tools and design methods for logic circuit implementation in plants. I highlighted recent and potential applications of those circuits to understand and engineer plant interaction with the environment, development, and metabolic pathways.
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Affiliation(s)
- Sarah Guiziou
- Engineering Biology, Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK.
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3
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Crayfish (Procambarus clarkii) TRPA1 is required for the defense against Aeromonas hydrophila infection under high temperature conditions and contributes to heat sensing. Comp Biochem Physiol B Biochem Mol Biol 2021; 257:110654. [PMID: 34371155 DOI: 10.1016/j.cbpb.2021.110654] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 07/18/2021] [Accepted: 08/03/2021] [Indexed: 11/20/2022]
Abstract
Temperature is an important environmental factor influencing immune responses of crayfish. However, the mechanism underlying how temperature affects immune responses remains unclear. Here, we identified an ortholog of the transient receptor potential ankyrin subtype 1 (TRPA1), a temperature sensor of Drosophila, from Procambarus clarkii (PcTRPA1-1). Its expression was induced by high temperature and challenge with heat-killed A. hydrophila at high temperature, but not at lower temperature. PcTRPA1-1 silencing led to increased mortality of crayfish challenged with live A. hydrophila at high temperature (32 °C), but had no statistically significant effect on crayfish mortality at 24 °C. This suggests that PcTRPA1-1 is involved in the immune responses of crayfish at high temperature as a potential temperature sensor. Further assay exhibited that PcTRPA1-1 silencing affected immune responses of crayfish, including increase of lipid peroxidation, reduction of total antioxidant capacity, decreased phenoloxidase activity and disruption of circadian rhythm of total hemocyte count entrained by temperature cycles. PcTRPA1-1 silencing also decreased the expression of PcHSP70 and PcHSP90 which are responsive to heat stimuli and bacterial challenge. The results collectively indicate that TRPA1 contributes to heat sensing of crayfish and is required for crayfish defense against bacterial infection.
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4
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Mol AA, Groher F, Schreiber B, Rühmkorff C, Suess B. Robust gene expression control in human cells with a novel universal TetR aptamer splicing module. Nucleic Acids Res 2020; 47:e132. [PMID: 31504742 PMCID: PMC6846422 DOI: 10.1093/nar/gkz753] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/15/2019] [Accepted: 08/20/2019] [Indexed: 01/12/2023] Open
Abstract
Fine-tuning of gene expression is desirable for a wide range of applications in synthetic biology. In this context, RNA regulatory devices provide a powerful and highly functional tool. We developed a versatile, robust and reversible device to control gene expression by splicing regulation in human cells using an aptamer that is recognized by the Tet repressor TetR. Upon insertion in proximity to the 5′ splice site, intron retention can be controlled via the binding of TetR to the aptamer. Although we were able to demonstrate regulation for different introns, the genomic context had a major impact on regulation. In consequence, we advanced the aptamer to develop a splice device. Our novel device contains the aptamer integrated into a context of exonic and intronic sequences that create and maintain an environment allowing a reliable and robust splicing event. The exon-born, additional amino acids will then be cleaved off by a self-cleaving peptide. This design allows portability of the splicing device, which we confirmed by demonstrating its functionality in different gene contexts. Intriguingly, our splicing device shows a high dynamic range and low basal activity, i.e. desirable features that often prove a major challenge when implementing synthetic biology in mammalian cell lines.
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Affiliation(s)
- Adam A Mol
- Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Florian Groher
- Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Britta Schreiber
- Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Ciaran Rühmkorff
- Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Beatrix Suess
- Department of Biology, Technical University of Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
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5
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Vogel M, Weigand JE, Kluge B, Grez M, Suess B. A small, portable RNA device for the control of exon skipping in mammalian cells. Nucleic Acids Res 2019; 46:e48. [PMID: 29420816 PMCID: PMC5934650 DOI: 10.1093/nar/gky062] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 01/29/2018] [Indexed: 12/17/2022] Open
Abstract
Splicing is an essential and highly regulated process in mammalian cells. We developed a synthetic riboswitch that efficiently controls alternative splicing of a cassette exon in response to the small molecule ligand tetracycline. The riboswitch was designed to control the accessibility of the 3' splice site by placing the latter inside the closing stem of a conformationally controlled tetracycline aptamer. In the presence of tetracycline, the cassette exon is skipped, whereas it is included in the ligand's absence. The design allows for an easy, context-independent integration of the regulatory device into any gene of interest. Portability of the device was shown through its functionality in four different systems: a synthetic minigene, a reporter gene and two endogenous genes. Furthermore, riboswitch functionality to control cellular signaling cascades was demonstrated by using it to specifically induce cell death through the conditionally controlled expression of CD20, which is a target in cancer therapy.
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Affiliation(s)
- Marc Vogel
- Department of Biology, Technical University Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Julia E Weigand
- Department of Biology, Technical University Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Britta Kluge
- Department of Biology, Technical University Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Manuel Grez
- Institute for Tumor Biology and Experimental Therapy, Georg-Speyer-Haus, Paul-Ehrlich-Str. 42-44, 60596 Frankfurt/M, Germany
| | - Beatrix Suess
- Department of Biology, Technical University Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
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6
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Pouvreau B, Vanhercke T, Singh S. From plant metabolic engineering to plant synthetic biology: The evolution of the design/build/test/learn cycle. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 273:3-12. [PMID: 29907306 DOI: 10.1016/j.plantsci.2018.03.035] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/19/2018] [Accepted: 03/28/2018] [Indexed: 05/21/2023]
Abstract
Genetic improvement of crops started since the dawn of agriculture and has continuously evolved in parallel with emerging technological innovations. The use of genome engineering in crop improvement has already revolutionised modern agriculture in less than thirty years. Plant metabolic engineering is still at a development stage and faces several challenges, in particular with the time necessary to develop plant based solutions to bio-industrial demands. However the recent success of several metabolic engineering approaches applied to major crops are encouraging and the emerging field of plant synthetic biology offers new opportunities. Some pioneering studies have demonstrated that synthetic genetic circuits or orthogonal metabolic pathways can be introduced into plants to achieve a desired function. The combination of metabolic engineering and synthetic biology is expected to significantly accelerate crop improvement. A defining aspect of both fields is the design/build/test/learn cycle, or the use of iterative rounds of testing modifications to refine hypotheses and develop best solutions. Several technological and technical improvements are now available to make a better use of each design, build, test, and learn components of the cycle. All these advances should facilitate the rapid development of a wide variety of bio-products for a world in need of sustainable solutions.
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Affiliation(s)
- Benjamin Pouvreau
- CSIRO Agriculture and Food, PO Box 1600, Canberra, ACT 2601, Australia.
| | - Thomas Vanhercke
- CSIRO Agriculture and Food, PO Box 1600, Canberra, ACT 2601, Australia
| | - Surinder Singh
- CSIRO Agriculture and Food, PO Box 1600, Canberra, ACT 2601, Australia
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7
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Suess B, Kemmerer K, Weigand JE. Splicing and Alternative Splicing Impact on Gene Design. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Beatrix Suess
- Department of Biology; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Germany
| | - Katrin Kemmerer
- Department of Biology; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Germany
| | - Julia E. Weigand
- Department of Biology; Technische Universität Darmstadt; Schnittspahnstraße 10 64287 Darmstadt Germany
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8
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Liang Y, Richardson S, Yan J, Benites VT, Cheng-Yue C, Tran T, Mortimer J, Mukhopadhyay A, Keasling JD, Scheller HV, Loqué D. Endoribonuclease-Based Two-Component Repressor Systems for Tight Gene Expression Control in Plants. ACS Synth Biol 2017; 6:806-816. [PMID: 28094975 DOI: 10.1021/acssynbio.6b00295] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Tight control and multifactorial regulation of gene expression are important challenges in genetic engineering and are critical for the development of regulatory circuits. Meeting these challenges will facilitate transgene expression regulation and support the fine-tuning of metabolic pathways to avoid the accumulation of undesired intermediates. By employing the endoribonuclease Csy4 and its recognition sequence from Pseudomonas aeruginosa and manipulating 5'UTR of mRNA, we developed a two-component expression-repression system to tightly control synthesis of transgene products. We demonstrated that this regulatory device was functional in monocotyledonous and dicotyledonous plant species, and showed that it can be used to repress transgene expression by >400-fold and to synchronize transgene repression. In addition to tissue-specific transgene repression, this system offers stimuli-dependent expression control. Using a bioinformatics approach, we identified 54 orthologous systems from various bacteria, and then validated in planta the activity for a few of those systems, demonstrating the potential diversity of such a two-component repressor system.
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Affiliation(s)
- Yan Liang
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis Street, 4th Floor, Emeryville, California 94608, United States
- Environmental
Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Sarah Richardson
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis Street, 4th Floor, Emeryville, California 94608, United States
- Environmental
Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Jingwei Yan
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis Street, 4th Floor, Emeryville, California 94608, United States
- Environmental
Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Veronica T. Benites
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis Street, 4th Floor, Emeryville, California 94608, United States
- Environmental
Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Clarabelle Cheng-Yue
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis Street, 4th Floor, Emeryville, California 94608, United States
- Environmental
Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Thu Tran
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis Street, 4th Floor, Emeryville, California 94608, United States
- Environmental
Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Jenny Mortimer
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis Street, 4th Floor, Emeryville, California 94608, United States
- Environmental
Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis Street, 4th Floor, Emeryville, California 94608, United States
- Environmental
Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Jay D. Keasling
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis Street, 4th Floor, Emeryville, California 94608, United States
- Environmental
Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Henrik V. Scheller
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis Street, 4th Floor, Emeryville, California 94608, United States
- Environmental
Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Dominique Loqué
- Joint BioEnergy Institute, EmeryStation East, 5885 Hollis Street, 4th Floor, Emeryville, California 94608, United States
- Environmental
Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
- INSA de Lyon, CNRS, UMR5240, Microbiologie,
Adaptation et Pathogénie, Université Claude Bernard Lyon 1, 10 rue Raphaël Dubois, F-69622, Villeurbanne, France
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9
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Shih PM, Liang Y, Loqué D. Biotechnology and synthetic biology approaches for metabolic engineering of bioenergy crops. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:103-17. [PMID: 27030440 DOI: 10.1111/tpj.13176] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 03/18/2016] [Accepted: 03/22/2016] [Indexed: 05/26/2023]
Abstract
The Green Revolution has fuelled an exponential growth in human population since the mid-20th century. Due to population growth, food and energy demands will soon surpass supply capabilities. To overcome these impending problems, significant improvements in genetic engineering will be needed to complement breeding efforts in order to accelerate the improvement of agronomical traits. The new field of plant synthetic biology has emerged in recent years and is expected to support rapid, precise, and robust engineering of plants. In this review, we present recent advances made in the field of plant synthetic biology, specifically in genome editing, transgene expression regulation, and bioenergy crop engineering, with a focus on traits related to lignocellulose, oil, and soluble sugars. Ultimately, progress and innovation in these fields may facilitate the development of beneficial traits in crop plants to meet society's bioenergy needs.
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Affiliation(s)
- Patrick M Shih
- Joint BioEnergy Institute, Emery Station East, 5885 Hollis St, 4th Floor, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Yan Liang
- Joint BioEnergy Institute, Emery Station East, 5885 Hollis St, 4th Floor, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Dominique Loqué
- Joint BioEnergy Institute, Emery Station East, 5885 Hollis St, 4th Floor, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
- Université Lyon 1, INSA de Lyon, CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, 10 rue Raphaël Dubois, F-69622, Villeurbanne, France
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10
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Min XJ, Powell B, Braessler J, Meinken J, Yu F, Sablok G. Genome-wide cataloging and analysis of alternatively spliced genes in cereal crops. BMC Genomics 2015; 16:721. [PMID: 26391769 PMCID: PMC4578763 DOI: 10.1186/s12864-015-1914-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 09/09/2015] [Indexed: 11/10/2022] Open
Abstract
Background Protein functional diversity at the post-transcriptional level is regulated through spliceosome mediated pre-mRNA alternative splicing (AS) events and that has been widely demonstrated to be a key player in regulating the functional diversity in plants. Identification and analysis of AS genes in cereal crop plants are critical for crop improvement and understanding regulatory mechanisms. Results We carried out the comparative analyses of the functional landscapes of the AS using the consensus assembly of expressed sequence tags and available mRNA sequences in four cereal plants. We identified a total of 8,734 in Oryza sativa subspecies (ssp) japonica, 2,657 in O. sativa ssp indica, 3,971 in Sorghum bicolor, and 10,687 in Zea mays AS genes. Among the identified AS events, intron retention remains to be the dominant type accounting for 23.5 % in S. bicolor, and up to 55.8 % in O. sativa ssp indica. We identified a total of 887 AS genes that were conserved among Z. mays, S. bicolor, and O. sativa ssp japonica; and 248 AS genes were found to be conserved among all four studied species or ssp. Furthermore, we identified 53 AS genes conserved with Brachypodium distachyon. Gene Ontology classification of AS genes revealed functional assignment of these genes in many biological processes with diverse molecular functions. Conclusions AS is common in cereal plants. The AS genes identified in four cereal crops in this work provide the foundation for further studying the roles of AS in regulation of cereal plant growth and development. The data can be accessed at Plant Alternative Splicing Database (http://proteomics.ysu.edu/altsplice/). Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1914-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiang Jia Min
- Department of Biological Sciences, Youngstown State University, Youngstown, OH, 44555, USA. .,Center for Applied Chemical Biology, Youngstown State University, Youngstown, OH, 44555, USA.
| | - Brian Powell
- Department of Computer Science and Information Systems, Youngstown State University, Youngstown, OH, 44555, USA
| | - Jonathan Braessler
- Department of Computer Science and Information Systems, Youngstown State University, Youngstown, OH, 44555, USA
| | - John Meinken
- Center for Applied Chemical Biology, Youngstown State University, Youngstown, OH, 44555, USA.,Department of Computer Science and Information Systems, Youngstown State University, Youngstown, OH, 44555, USA.,Present address: Center for Health Informatics, University of Cincinnati, Cincinnati, OH, 45267-0840, USA
| | - Feng Yu
- Department of Computer Science and Information Systems, Youngstown State University, Youngstown, OH, 44555, USA
| | - Gaurav Sablok
- Plant Functional Biology and Climate Change Cluster (C3), University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
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11
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Gonzalez TL, Liang Y, Nguyen BN, Staskawicz BJ, Loqué D, Hammond MC. Tight regulation of plant immune responses by combining promoter and suicide exon elements. Nucleic Acids Res 2015; 43:7152-61. [PMID: 26138488 PMCID: PMC4538838 DOI: 10.1093/nar/gkv655] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 06/12/2015] [Accepted: 06/16/2015] [Indexed: 11/20/2022] Open
Abstract
Effector-triggered immunity (ETI) is activated when plant disease resistance (R) proteins recognize the presence of pathogen effector proteins delivered into host cells. The ETI response generally encompasses a defensive 'hypersensitive response' (HR) that involves programmed cell death at the site of pathogen recognition. While many R protein and effector protein pairs are known to trigger HR, other components of the ETI signaling pathway remain elusive. Effector genes regulated by inducible promoters cause background HR due to leaky protein expression, preventing the generation of relevant transgenic plant lines. By employing the HyP5SM suicide exon, we have developed a strategy to tightly regulate effector proteins such that HR is chemically inducible and non-leaky. This alternative splicing-based gene regulation system was shown to successfully control Bs2/AvrBs2-dependent and RPP1/ATR1Δ51-dependent HR in Nicotiana benthamiana and Nicotiana tabacum, respectively. It was also used to generate viable and healthy transgenic Arabidopsis thaliana plants that inducibly initiate HR. Beyond enabling studies on the ETI pathway, our regulatory strategy is generally applicable to reduce or eliminate undesired background expression of transgenes.
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Affiliation(s)
- Tania L Gonzalez
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Yan Liang
- Joint BioEnergy Institute, 5885 Hollis St, Emeryville, CA 94608, USA Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Bao N Nguyen
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Brian J Staskawicz
- Department of Plant & Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Dominique Loqué
- Joint BioEnergy Institute, 5885 Hollis St, Emeryville, CA 94608, USA Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ming C Hammond
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA Department of Chemistry, University of California, Berkeley, CA 94720, USA
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12
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Mahfouz MM, Piatek A, Stewart CN. Genome engineering via TALENs and CRISPR/Cas9 systems: challenges and perspectives. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:1006-14. [PMID: 25250853 DOI: 10.1111/pbi.12256] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Revised: 08/07/2014] [Accepted: 08/14/2014] [Indexed: 05/07/2023]
Abstract
The ability to precisely modify genome sequence and regulate gene expression patterns in a site-specific manner holds much promise in plant biotechnology. Genome-engineering technologies that enable such highly specific and efficient modification are advancing with unprecedented pace. Transcription activator-like effectors (TALEs) provide customizable DNA-binding modules designed to bind to any sequence of interest. Thus, TALEs have been used as a DNA targeting module fused to functional domains for a variety of targeted genomic and epigenomic modifications. TALE nucleases (TALENs) have been used with much success across eukaryotic species to edit genomes. Recently, clustered regularly interspaced palindromic repeats (CRISPRs) that are used as guide RNAs for Cas9 nuclease-specific digestion has been introduced as a highly efficient DNA-targeting platform for genome editing and regulation. Here, we review the discovery, development and limitations of TALENs and CRIPSR/Cas9 systems as genome-engineering platforms in plants. We discuss the current questions, potential improvements and the development of the next-generation genome-editing platforms with an emphasis on producing designer plants to address the needs of agriculture and basic plant biology.
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Affiliation(s)
- Magdy M Mahfouz
- Division of Biological Sciences & Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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13
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Mattozzi MD, Voges MJ, Silver PA, Way JC. Transient gene expression in tobacco using Gibson assembly and the Gene Gun. J Vis Exp 2014:51234. [PMID: 24796418 PMCID: PMC4172236 DOI: 10.3791/51234] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
In order to target a single protein to multiple subcellular organelles, plants typically duplicate the relevant genes, and express each gene separately using complex regulatory strategies including differential promoters and/or signal sequences. Metabolic engineers and synthetic biologists interested in targeting enzymes to a particular organelle are faced with a challenge: For a protein that is to be localized to more than one organelle, the engineer must clone the same gene multiple times. This work presents a solution to this strategy: harnessing alternative splicing of mRNA. This technology takes advantage of established chloroplast and peroxisome targeting sequences and combines them into a single mRNA that is alternatively spliced. Some splice variants are sent to the chloroplast, some to the peroxisome, and some to the cytosol. Here the system is designed for multiple-organelle targeting with alternative splicing. In this work, GFP was expected to be expressed in the chloroplast, cytosol, and peroxisome by a series of rationally designed 5' mRNA tags. These tags have the potential to reduce the amount of cloning required when heterologous genes need to be expressed in multiple subcellular organelles. The constructs were designed in previous work(11), and were cloned using Gibson assembly, a ligation independent cloning method that does not require restriction enzymes. The resultant plasmids were introduced into Nicotiana benthamiana epidermal leaf cells with a modified Gene Gun protocol. Finally, transformed leaves were observed with confocal microscopy.
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Affiliation(s)
- Matthew D Mattozzi
- Synthetic Biology Platform, Wyss Institute for Biologically Inspired Engineering, Harvard University; Department of Systems Biology, Harvard Medical School;
| | - Mathias J Voges
- Synthetic Biology Platform, Wyss Institute for Biologically Inspired Engineering, Harvard University; Department of Systems Biology, Harvard Medical School; Department of Biotechnology, Delft University of Technology
| | - Pamela A Silver
- Synthetic Biology Platform, Wyss Institute for Biologically Inspired Engineering, Harvard University; Department of Systems Biology, Harvard Medical School
| | - Jeffrey C Way
- Synthetic Biology Platform, Wyss Institute for Biologically Inspired Engineering, Harvard University; Department of Systems Biology, Harvard Medical School
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14
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Lignin bioengineering. Curr Opin Biotechnol 2014; 26:189-98. [DOI: 10.1016/j.copbio.2014.01.002] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2013] [Revised: 12/24/2013] [Accepted: 01/06/2014] [Indexed: 01/08/2023]
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15
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Reddy AS, Marquez Y, Kalyna M, Barta A. Complexity of the alternative splicing landscape in plants. THE PLANT CELL 2013; 25:3657-83. [PMID: 24179125 PMCID: PMC3877793 DOI: 10.1105/tpc.113.117523] [Citation(s) in RCA: 516] [Impact Index Per Article: 46.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2013] [Revised: 09/27/2013] [Accepted: 10/08/2013] [Indexed: 05/18/2023]
Abstract
Alternative splicing (AS) of precursor mRNAs (pre-mRNAs) from multiexon genes allows organisms to increase their coding potential and regulate gene expression through multiple mechanisms. Recent transcriptome-wide analysis of AS using RNA sequencing has revealed that AS is highly pervasive in plants. Pre-mRNAs from over 60% of intron-containing genes undergo AS to produce a vast repertoire of mRNA isoforms. The functions of most splice variants are unknown. However, emerging evidence indicates that splice variants increase the functional diversity of proteins. Furthermore, AS is coupled to transcript stability and translation through nonsense-mediated decay and microRNA-mediated gene regulation. Widespread changes in AS in response to developmental cues and stresses suggest a role for regulated splicing in plant development and stress responses. Here, we review recent progress in uncovering the extent and complexity of the AS landscape in plants, its regulation, and the roles of AS in gene regulation. The prevalence of AS in plants has raised many new questions that require additional studies. New tools based on recent technological advances are allowing genome-wide analysis of RNA elements in transcripts and of chromatin modifications that regulate AS. Application of these tools in plants will provide significant new insights into AS regulation and crosstalk between AS and other layers of gene regulation.
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Affiliation(s)
- Anireddy S.N. Reddy
- Department of Biology, Program in Molecular Plant Biology, Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523
- Address correspondence to
| | - Yamile Marquez
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna A-1030, Austria
| | - Maria Kalyna
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna A-1030, Austria
| | - Andrea Barta
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna A-1030, Austria
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16
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Walters B, Lum G, Sablok G, Min XJ. Genome-wide landscape of alternative splicing events in Brachypodium distachyon. DNA Res 2013; 20:163-71. [PMID: 23297300 PMCID: PMC3628446 DOI: 10.1093/dnares/dss041] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 12/12/2012] [Indexed: 01/23/2023] Open
Abstract
Recently, Brachypodium distachyon has emerged as a model plant for studying monocot grasses and cereal crops. Using assembled expressed transcript sequences and subsequent mapping to the corresponding genome, we identified 1219 alternative splicing (AS) events spanning across 2021 putatively assembled transcripts generated from 941 genes. Approximately, 6.3% of expressed genes are alternatively spliced in B. distachyon. We observed that a majority of the identified AS events were related to retained introns (55.5%), followed by alternative acceptor sites (16.7%). We also observed a low percentage of exon skipping (5.0%) and alternative donor site events (8.8%). The 'complex event' that consists of a combination of two or more basic splicing events accounted for ∼14.0%. Comparative AS transcript analysis revealed 163 and 39 homologous pairs between B. distachyon and Oryza sativa and between B. distachyon and Arabidopsis thaliana, respectively. In all, we found 16 AS transcripts to be conserved in all 3 species. AS events and related putative assembled transcripts annotation can be systematically browsed at Plant Alternative Splicing Database (http://proteomics.ysu.edu/altsplice/plant/).
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Affiliation(s)
- Braden Walters
- Department of Computer Science and Information Systems, Youngstown State University, Youngstown, OH 44555, USA
| | - Gengkon Lum
- Department of Computer Science and Information Systems, Youngstown State University, Youngstown, OH 44555, USA
| | - Gaurav Sablok
- Sustainable Agro-ecosystems and Bioresources Department, IASMA Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, San Michele all'Adige, Trentino 38010, Italy
| | - Xiang Jia Min
- Center for Applied Chemical Biology, Department of Biological Sciences, Youngstown State University, Youngstown, OH 44555, USA
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