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Koukara J, Papadopoulou KK. Advances in plant synthetic biology approaches to control expression of gene circuits. Biochem Biophys Res Commun 2023; 654:55-61. [PMID: 36889035 DOI: 10.1016/j.bbrc.2023.02.061] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 02/22/2023] [Indexed: 03/08/2023]
Abstract
The applications of synthetic biology range from creating simple circuits to monitor an organism's state to complex circuits capable of reconstructing aspects of life. The latter has the potential to be used in plant synthetic biology to address current societal issues by reforming agriculture and enhancing production of molecules of increased demand. For this reason, development of efficient tools to precisely control gene expression of circuits must be prioritized. In this review, we report the latest efforts towards characterization, standardization and assembly of genetic parts into higher-order constructs, as well as available types of inducible systems to modulate their transcription in plant systems. Subsequently, we discuss recent developments in the orthogonal control of gene expression, Boolean logic gates and synthetic genetic toggle-like switches. Finally, we conclude that by combining different means of controlling gene expression, we can create complex circuits capable of reshaping plant life.
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Affiliation(s)
- Jenny Koukara
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece
| | - Kalliope K Papadopoulou
- Laboratory of Plant and Environmental Biotechnology, Department of Biochemistry and Biotechnology, University of Thessaly, Larissa, Greece.
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Yasmeen E, Wang J, Riaz M, Zhang L, Zuo K. Designing artificial synthetic promoters for accurate, smart, and versatile gene expression in plants. PLANT COMMUNICATIONS 2023:100558. [PMID: 36760129 PMCID: PMC10363483 DOI: 10.1016/j.xplc.2023.100558] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
With the development of high-throughput biology techniques and artificial intelligence, it has become increasingly feasible to design and construct artificial biological parts, modules, circuits, and even whole systems. To overcome the limitations of native promoters in controlling gene expression, artificial promoter design aims to synthesize short, inducible, and conditionally controlled promoters to coordinate the expression of multiple genes in diverse plant metabolic and signaling pathways. Synthetic promoters are versatile and can drive gene expression accurately with smart responses; they show potential for enhancing desirable traits in crops, thereby improving crop yield, nutritional quality, and food security. This review first illustrates the importance of synthetic promoters, then introduces promoter architecture and thoroughly summarizes advances in synthetic promoter construction. Restrictions to the development of synthetic promoters and future applications of such promoters in synthetic plant biology and crop improvement are also discussed.
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Affiliation(s)
- Erum Yasmeen
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Riaz
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lida Zhang
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kaijing Zuo
- Single Cell Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
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Huang D, Kosentka PZ, Liu W. Synthetic biology approaches in regulation of targeted gene expression. CURRENT OPINION IN PLANT BIOLOGY 2021; 63:102036. [PMID: 33930839 DOI: 10.1016/j.pbi.2021.102036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 05/15/2023]
Abstract
Synthetic biology approaches are highly sought-after to facilitate the regulation of targeted gene expression in plants for functional genomics research and crop trait improvement. To date, synthetic regulation of gene expression predominantly focuses at the transcription level via engineering of synthetic promoters and transcription factors, while pioneering examples have started to emerge for synthetic regulation of gene expression at the levels of mRNA stability, translation, and protein degradation. This review discusses recent advances in plant synthetic biology for the regulation of gene expression at multiple levels, and highlights their future directions.
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Affiliation(s)
- Debao Huang
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
| | - Pawel Z Kosentka
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA
| | - Wusheng Liu
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27607, USA.
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Li W, Liu B, Zhao M, Zhang K, He Q, Zhao X, Cheng W, Ding Z, Zhang K, Li K. Isolation and characterization of a 295-bp strong promoter of maize high-affinity phosphate transporter gene ZmPht1; 5 in transgenic Nicotiana benthamiana and Zea mays. PLANTA 2020; 251:106. [PMID: 32424449 DOI: 10.1007/s00425-020-03400-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 05/06/2020] [Indexed: 06/11/2023]
Abstract
MAIN CONCLUSION The small 295-bp ZmPht1; 5 promoter is sufficient to drive high-intensity expression of target genes, especially under phosphate deprivation conditions, and is therefore useful for crop improvement via transgenic techniques. Phosphate (Pi) deficiency has become a major challenge and limiting factor in world agricultural production. Manipulating the gene expression using appropriate promoters to improve the Pi absorption and utilization efficiency of crops could reduce the requirement for Pi fertilizers. In the study, a 295-bp strong promoter (M2P-7) of maize high-affinity phosphate transporter ZmPht1; 5 was isolated and functionally validated in transgenic Nicotiana benthamiana and maize by analyzing the ZmPht1; 5 promoter (M2P-1) and its 5' truncated variants (M2P-2 ~ M2P-8) in different sizes under normal and Pi-deprivation conditions. The M2P-7 displayed the highest promoter activities among 5' truncated fragments in all tested tissues of transgenic Nicotiana benthamiana at different development stages, which was 1.5 and 3 times higher than the well-used CaMV35S promoter under normal and Pi-deprivation conditions, respectively. In maize, the M2P-7 promoter activity was comparable to the maize ubiquitin1 promoter widely used in monocots under normal condition, which was about 1.3 times that of the ubiquitin1 promoter under Pi-deprivation environments. Moreover, the M2P-7 fragment is only 295 bp in length, thus reducing the construct size, and is therefore beneficial for genetic transformation. Thus, the small promoter M2P-7 of plant origin could be of great use for monocotyledonous and dicotyledonous crop improvement via transgenic techniques based on its promoter activities, expression patterns and small size.
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Affiliation(s)
- Wendi Li
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Baiyu Liu
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Mengsha Zhao
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Ke Zhang
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Qiuxia He
- Biology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, China
| | - Xiangyu Zhao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Wen Cheng
- Maize Institute of Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
| | - Zhaohua Ding
- Maize Institute of Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
| | - Kewei Zhang
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Kunpeng Li
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao, 266237, China.
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Dash A, Gurdaswani V, D'Souza JS, Ghag SB. Functional characterization of an inducible bidirectional promoter from Fusarium oxysporum f. sp. cubense. Sci Rep 2020; 10:2323. [PMID: 32047173 PMCID: PMC7012866 DOI: 10.1038/s41598-020-59159-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 01/16/2020] [Indexed: 01/27/2023] Open
Abstract
Bidirectional promoters (BDPs) are regulatory DNA sequences (~1000 bp long) intervening two genes arranged on opposite strands with their 5' ends in close proximity. These genes are mostly co-expressed; but, instances of anti-correlation and independent transcription have been observed. In fungal systems, BDPs have shown to provide an improved genetic circuit by assembling and regulating transcription of different genes of a common metabolic pathway. We have identified an intergenic region (1063 bp) from the genome of Fusarium oxysporum f. sp. cubense (Foc), a banana root pathogen. This intergenic region regulates the expression of a gene pair required for the breakdown of hemicellulose. For characterization, it was cloned into pCSN44 vector backbone between two reporter genes, namely β-glucuronidase (GUS) and enhanced green fluorescent protein (EGFP). The newly formed vector was transformed into Foc and tested for its bidirectional expression activity. Using histochemical staining and fluorescence microscopy, the kinetics for both, GUS and EGFP expression were tested under different growth conditions respectively. The activity was differentially regulated by inducers such as xylan, arabinogalactan and pectin. This is the first report on the isolation of the intergenic region with inducible bidirectional promoter activity from Fusarium. Characterization of such BDPs will find applications in genetic engineering, metabolic engineering and synthetic biology using fungal systems.
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Affiliation(s)
- Ashutosh Dash
- School of Biological Sciences, UM-DAE Centre for Excellence in Basic Sciences, Kalina campus, Santacruz (East), Mumbai, 400098, India
| | - Vartika Gurdaswani
- School of Biological Sciences, UM-DAE Centre for Excellence in Basic Sciences, Kalina campus, Santacruz (East), Mumbai, 400098, India
| | - Jacinta S D'Souza
- School of Biological Sciences, UM-DAE Centre for Excellence in Basic Sciences, Kalina campus, Santacruz (East), Mumbai, 400098, India
| | - Siddhesh B Ghag
- School of Biological Sciences, UM-DAE Centre for Excellence in Basic Sciences, Kalina campus, Santacruz (East), Mumbai, 400098, India.
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