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Park SJ, Park JS, Yang JH, Moon KB, Shin SY, Jeon JH, Kim HS, Lee HJ. MicroRNA396 negatively regulates shoot regeneration in tomato. Hortic Res 2024; 11:uhad291. [PMID: 38371631 PMCID: PMC10873581 DOI: 10.1093/hr/uhad291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 12/19/2023] [Indexed: 02/20/2024]
Abstract
Numerous studies have been dedicated to genetically engineering crops to enhance their yield and quality. One of the key requirements for generating genetically modified plants is the reprogramming of cell fate. However, the efficiency of shoot regeneration during this process is highly dependent on genotypes, and the underlying molecular mechanisms remain poorly understood. Here, we identified microRNA396 (miR396) as a negative regulator of shoot regeneration in tomato. By selecting two genotypes with contrasting shoot regeneration efficiencies and analyzing their transcriptome profiles, we found that miR396 and its target transcripts, which encode GROWTH-REGULATING FACTORs (GRFs), exhibit differential abundance between high- and low-efficiency genotypes. Suppression of miR396 functions significantly improved shoot regeneration rates along with increased expression of GRFs in transformed T0 explants, suggesting that miR396 is a key molecule involved in the determination of regeneration efficiency. Notably, we also showed that co-expression of a miR396 suppressor with the gene-editing tool can be employed to generate gene-edited plants in the genotype with a low capacity for shoot regeneration. Our findings show the critical role of miR396 as a molecular barrier to shoot regeneration in tomato and suggest that regeneration efficiency can be improved by blocking this single microRNA.
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Affiliation(s)
- Su-Jin Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, 125 Gwahak-ro, Daejeon 34113, Korea
| | - Ji-Sun Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
| | - Jin Ho Yang
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
| | - Ki-Beom Moon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
| | - Seung Yong Shin
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, 125 Gwahak-ro, Daejeon 34113, Korea
| | - Jae-Heung Jeon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, 125 Gwahak-ro, Daejeon 34113, Korea
| | - Hyo-Jun Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Daejeon 34141, Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, 125 Gwahak-ro, Daejeon 34113, Korea
- Department of Biological Sciences, Sungkyunkwan University, 2066 Seobu-ro, Suwon 16419, Korea
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Kannan P, Oh J, Yeon YJ, Park YI, Seo MH, Park K. Computational identification of key residues regulating fluorescence emission in a red/green cyanobacteriochrome. Proteins 2024; 92:106-116. [PMID: 37646483 DOI: 10.1002/prot.26586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/03/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023]
Abstract
Cyanobacteriochromes (CBCRs) are linear tetrapyrrole bilin-binding photoreceptors of cyanobacteria that exhibit high spectral diversity, gaining attention in optogenetics and bioimaging applications. Several engineering studies on CBCRs were attempted, especially for designing near-infrared (NIR) fluorescent proteins with longer fluorescence wavelengths. However, despite continuous efforts, a key component regulating fluorescence emission property in CBCRs is still poorly understood. As a model system, we focused on red/green CBCR Slr1393g3, from the unicellular cyanobacterium Synechocystis sp. PCC 6803 to engineer Pr to get far-red light-emitting property. Energy profiling and pairwise structural comparison of Slr1393g3 variants effectively reveal the mutations that are critical to the fluorescence changes. H497 seems to play a key role in stabilizing the chromophore environment, especially the α3 helix, while H495, T499, and Q502 are potential key residues determining fluorescence emission peak wavelength. We also found that mutations of α2 and α4 helical regions are closely related to the chromophore binding stability and likely affect fluorescence properties. Taken together, our computational analysis suggests that the fluorescence of Slr1393g3 is mainly controlled by the stabilization of the chromophore binding pocket. The predicted key residues potentially regulating the fluorescence emission property of a red/green CBCR will be advantageous for designing improved NIR fluorescent protein when combined with in vitro molecular evolution approaches.
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Affiliation(s)
- Priyadharshini Kannan
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangneung, Republic of Korea
- Department of Biochemical Engineering, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Jisung Oh
- Department of Biochemical Engineering, Gangneung-Wonju National University, Gangneung, Republic of Korea
- Natural Product Research Center, Korea Institute of Science and Technology, Gangneung, Republic of Korea
| | - Young Joo Yeon
- Department of Biochemical Engineering, Gangneung-Wonju National University, Gangneung, Republic of Korea
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon, Republic of Korea
| | - Moon-Hyeong Seo
- Natural Product Research Center, Korea Institute of Science and Technology, Gangneung, Republic of Korea
- Department of Convergence Medicine, Wonju Severance Christian Hospital, Yonsei University Wonju College of Medicine, Wonju, Republic of Korea
- Department of YM-KIST Bio-Health Convergence, Yonsei University, Wonju, Republic of Korea
| | - Keunwan Park
- Natural Product Informatics Research Center, Korea Institute of Science and Technology, Gangneung, Republic of Korea
- Department of YM-KIST Bio-Health Convergence, Yonsei University, Wonju, Republic of Korea
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