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Fan N, Su L, Lv A, Wen W, Gao L, You X, Zhou P, An Y. PECTIN ACETYLESTERASE12 regulates shoot branching via acetic acid and auxin accumulation in alfalfa shoots. PLANT PHYSIOLOGY 2024; 195:518-533. [PMID: 38365203 DOI: 10.1093/plphys/kiae071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 12/06/2023] [Accepted: 12/24/2023] [Indexed: 02/18/2024]
Abstract
Shoot branching is an important biological trait affecting alfalfa (Medicago sativa L.) production, but its development is complicated and the mechanism is not fully clear. In the present study, pectin acetylesterase 12 (MsPAE12) and NAM/ATAF/CUC-domain transcription factor gene (MsNAC73) were isolated from alfalfa. MsPAE12 was highly expressed in shoot apexes, and MsNAC73 was found to be a key transcriptional repressor of MsPAE12 by directly binding to salicylic acid (SA) and jasmonic acid (JA) elements in the MsPAE12 promoter. The biological functions of MsPAE12 and MsNAC73 were studied through overexpression (OE) and down-expression (RNAi) of the 2 genes in alfalfa. The numbers of shoot branches increased in MsPAE12-OE lines but decreased in MsPAE12-RNAi and MsNAC73-OE plants, which was negatively related to their indole-3-acetic acid (IAA) accumulation in shoot apexes. Furthermore, the contents of acetic acid (AA) in shoot apexes decreased in MsPAE12-OE plants but increased in MsPAE12-RNAi and MsNAC73-OE plants. The changes of AA contents were positively related to the expression of TRYPTOPHAN AMINOTRANSFERASE 1 (MsTAA1), TRYPTOPHAN AMINOTRANSFERASE-RELATED 2 (MsTAR2), and YUCCA flavin monooxygenase (MsYUCC4) and the contents of tryptophan (Trp), indole-3-pyruvic acid (IPA), and IAA in shoot apexes of MsPAE12-OE, MsPAE12-RNAi, and MsNAC73-OE plants. Exogenous application of AA to wild type (WT) and MsPAE12-OE plants increased Trp, IPA, and IAA contents and decreased branch number. Exogenous IAA suppressed shoot branching in MsPAE12-OE plants, but exogenous IAA inhibitors increased shoot branching in MsPAE12-RNAi plants. These results indicate that the MsNAC73-MsPAE12 module regulates auxin-modulated shoot branching via affecting AA accumulation in shoot apexes of alfalfa.
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Affiliation(s)
- Nana Fan
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- College of Life Science, Yulin University, Yulin 719000, China
| | - Liantai Su
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Aimin Lv
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Wuwu Wen
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Li Gao
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiangkai You
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Peng Zhou
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuan An
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
- Key Laboratory of Urban Agriculture, Ministry of Agriculture, Shanghai 201101, China
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2
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Li C, Hou X, Zhao Z, Liu H, Huang P, Shi M, Wu X, Gao R, Liu Z, Wei L, Li Y, Liao W. A tomato NAC transcription factor, SlNAP1, directly regulates gibberellin-dependent fruit ripening. Cell Mol Biol Lett 2024; 29:57. [PMID: 38649857 PMCID: PMC11036752 DOI: 10.1186/s11658-024-00577-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 04/09/2024] [Indexed: 04/25/2024] Open
Abstract
In tomato (Solanum lycopersicum), the ripening of fruit is regulated by the selective expression of ripening-related genes, and this procedure is controlled by transcription factors (TFs). In the various plant-specific TF families, the no apical meristem (NAM), Arabidopsis thaliana activating factor 1/2 (ATAF1/2), and cup-shaped cotyledon 2 (CUC2; NAC) TF family stands out and plays a significant function in plant physiological activities, such as fruit ripening (FR). Despite the numerous genes of NAC found in the tomato genome, limited information is available on the effects of NAC members on FR, and there is also a lack of studies on their target genes. In this research, we focus on SlNAP1, which is a NAC TF that positively influences the FR of tomato. By employing CRISPR/Cas9 technology, compared with the wild type (WT), we generated slnap1 mutants and observed a delay in the ethylene production and color change of fruits. We employed the yeast one-hybrid (Y1H) and dual-luciferase reporter (DLR) assays to confirm that SlNAP1 directly binds to the promoters of two crucial genes involved in gibberellin (GA) degradation, namely SlGA2ox1 and SlGA2ox5, thus activating their expression. Furthermore, through a yeast two-hybrid (Y2H), bimolecular fluorescence complementation (BIFC) and luciferase (LUC) assays, we established an interaction between SlNAP1 and SlGID1. Hence, our findings suggest that SlNAP1 regulates FR positively by activating the GA degradation genes directly. Additionally, the interaction between SlNAP1 and SlGID1 may play a role in SlNAP1-induced FR. Overall, our study provides important insights into the molecular mechanisms through which NAC TFs regulate tomato FR via the GA pathway.
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Affiliation(s)
- Changxia Li
- College of Horticulture, Gansu Agricultural University, 1 Yinmen Village, Anning District, Lanzhou, 730070, China
- College of Agriculture, Guangxi University, 100 East University Road, Xixiangtang District, Nanning, 530004, China
| | - Xuemei Hou
- College of Horticulture, Gansu Agricultural University, 1 Yinmen Village, Anning District, Lanzhou, 730070, China
| | - Zongxi Zhao
- College of Horticulture, Gansu Agricultural University, 1 Yinmen Village, Anning District, Lanzhou, 730070, China
| | - Huwei Liu
- College of Horticulture, Gansu Agricultural University, 1 Yinmen Village, Anning District, Lanzhou, 730070, China
| | - Panpan Huang
- College of Horticulture, Gansu Agricultural University, 1 Yinmen Village, Anning District, Lanzhou, 730070, China
| | - Meimei Shi
- College of Horticulture, Gansu Agricultural University, 1 Yinmen Village, Anning District, Lanzhou, 730070, China
| | - Xuetong Wu
- College of Horticulture, Gansu Agricultural University, 1 Yinmen Village, Anning District, Lanzhou, 730070, China
| | - Rong Gao
- College of Horticulture, Gansu Agricultural University, 1 Yinmen Village, Anning District, Lanzhou, 730070, China
| | - Zhiya Liu
- College of Horticulture, Gansu Agricultural University, 1 Yinmen Village, Anning District, Lanzhou, 730070, China
| | - Lijuan Wei
- Spice Crops Research Institute, College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, China
| | - Yihua Li
- College of Horticulture, Gansu Agricultural University, 1 Yinmen Village, Anning District, Lanzhou, 730070, China
| | - Weibiao Liao
- College of Horticulture, Gansu Agricultural University, 1 Yinmen Village, Anning District, Lanzhou, 730070, China.
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3
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Cao X, Li X, Su Y, Zhang C, Wei C, Chen K, Grierson D, Zhang B. Transcription factor PpNAC1 and DNA demethylase PpDML1 synergistically regulate peach fruit ripening. PLANT PHYSIOLOGY 2024; 194:2049-2068. [PMID: 37992120 DOI: 10.1093/plphys/kiad627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/24/2023]
Abstract
Fruit ripening is accompanied by dramatic changes in color, texture, and flavor and is regulated by transcription factors (TFs) and epigenetic factors. However, the detailed regulatory mechanism remains unclear. Gene expression patterns suggest that PpNAC1 (NAM/ATAF1/2/CUC) TF plays a major role in peach (Prunus persica) fruit ripening. DNA affinity purification (DAP)-seq combined with transactivation tests demonstrated that PpNAC1 can directly activate the expression of multiple ripening-related genes, including ACC synthase1 (PpACS1) and ACC oxidase1 (PpACO1) involved in ethylene biosynthesis, pectinesterase1 (PpPME1), pectate lyase1 (PpPL1), and polygalacturonase1 (PpPG1) related to cell wall modification, and lipase1 (PpLIP1), fatty acid desaturase (PpFAD3-1), and alcohol acyltransferase1 (PpAAT1) involved in volatiles synthesis. Overexpression of PpNAC1 in the tomato (Solanum lycopersicum) nor (nonripening) mutant restored fruit ripening, and its transient overexpression in peach fruit induced target gene expression, supporting a positive role of PpNAC1 in fruit ripening. The enhanced transcript levels of PpNAC1 and its target genes were associated with decreases in their promoter mCG methylation during ripening. Declining DNA methylation was negatively associated with increased transcripts of DNA demethylase1 (PpDML1), whose promoter is recognized and activated by PpNAC1. We propose that decreased methylation of the promoter region of PpNAC1 leads to a subsequent decrease in DNA methylation levels and enhanced transcription of ripening-related genes. These results indicate that positive feedback between PpNAC1 and PpDML1 plays an important role in directly regulating expression of multiple genes required for peach ripening and quality formation.
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Affiliation(s)
- Xiangmei Cao
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Xinzhao Li
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Yike Su
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Chi Zhang
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Chunyan Wei
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Desheng Middle Road No. 298, Hangzhou, Zhejiang Province 310021, China
| | - Kunsong Chen
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Donald Grierson
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Bo Zhang
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
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Gapper NE. NACs strike again: NOR-like1 is responsible for cuticle development in tomato fruit. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1791-1795. [PMID: 38534188 DOI: 10.1093/jxb/erae049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
This article comments on:
Liu G-S, Huang H, Grierson D, Gao Y, Ji X, Peng Z-Z, Li H-L, Niu X-L, Jia W, He J-L, Xiang L-T, Gao H-Y, Qu G-Q, Zhu H-L, Zhu B-Z, Luo Y-B, Fu D-Q. 2024. NAC transcription factor SlNOR-like1 plays a dual regulatory role in tomato fruit cuticle formation. Journal of Experimental Botany 75, 1903–1918.
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Affiliation(s)
- Nigel E Gapper
- The New Zealand Institute for Plant and Food Research Limited, Mount Albert Research Centre, Auckland, New Zealand
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5
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Niu MX, Feng CH, He F, Zhang H, Bao Y, Liu SJ, Liu X, Su Y, Liu C, Wang HL, Yin W, Xia X. The miR6445-NAC029 module regulates drought tolerance by regulating the expression of glutathione S-transferase U23 and reactive oxygen species scavenging in Populus. THE NEW PHYTOLOGIST 2024. [PMID: 38515251 DOI: 10.1111/nph.19703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 03/06/2024] [Indexed: 03/23/2024]
Abstract
MicroRNAs are essential in plant development and stress resistance, but their specific roles in drought stress require further investigation. Here, we have uncovered that a Populus-specific microRNAs (miRNA), miR6445, targeting NAC (NAM, ATAF, and CUC) family genes, is involved in regulating drought tolerance of poplar. The expression level of miR6445 was significantly upregulated under drought stress; concomitantly, seven targeted NAC genes showed significant downregulation. Silencing the expression of miR6445 by short tandem target mimic technology significantly decreased the drought tolerance in poplar. Furthermore, 5' RACE experiments confirmed that miR6445 directly targeted NAC029. The overexpression lines of PtrNAC029 (OE-NAC029) showed increased sensitivity to drought compared with knockout lines (Crispr-NAC029), consistent with the drought-sensitive phenotype observed in miR6445-silenced strains. PtrNAC029 was further verified to directly bind to the promoters of glutathione S-transferase U23 (GSTU23) and inhibit its expression. Both Crispr-NAC029 and PtrGSTU23 overexpressing plants showed higher levels of PtrGSTU23 transcript and GST activity while accumulating less reactive oxygen species (ROS). Moreover, poplars overexpressing GSTU23 demonstrated enhanced drought tolerance. Taken together, our research reveals the crucial role of the miR6445-NAC029-GSTU23 module in enhancing poplar drought tolerance by regulating ROS homeostasis. This finding provides new molecular targets for improving the drought resistance of trees.
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Affiliation(s)
- Meng-Xue Niu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Cong-Hua Feng
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Fang He
- Key Laboratory of National Forestry & Grassland Administration on Forest Resources Conservation and Ecological Safety in the Upper Reaches of the Yangtze River, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Han Zhang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yu Bao
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Shu-Jing Liu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xiao Liu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yanyan Su
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Chao Liu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Hou-Ling Wang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Weilun Yin
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xinli Xia
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
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Zhang Y, Pu Y, Jiang H, Chen L, Shen C, Zhang W, Cao J, Jiang W. Improved sustained-release properties of ginger essential oil in a Pickering emulsion system incorporated in sodium alginate film and delayed postharvest senescence of mango fruits. Food Chem 2024; 435:137534. [PMID: 37769562 DOI: 10.1016/j.foodchem.2023.137534] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/18/2023] [Accepted: 09/18/2023] [Indexed: 10/03/2023]
Abstract
The insufficient water vapor barrier and mechanical capacity of sodium alginate (SA) film limited its application in fruit preservation. Herein, cellulose nanocrystals (CNCs) were used to stabilize Pickering emulsion. Then, we prepared SA composite films. Ginger essential oil (GEO) was loaded as antimicrobials and antioxidants. Finally, the application on mangos were investigated. Compared to coarse emulsion, Pickering emulsion and its film-formation-solution showed more stable system and larger droplet size. The emulsion significantly changed the properties of SA film. Specifically, CNCs improved the thermal, tensile, and barrier properties of the film and GEO enhanced the ultraviolet-visible light barrier capacity. Additionally, the SA/CNC film possessed a homogeneous micromorphology which had a sustained-release effect on GEO, thus maintaining high postharvest quality and long-term bioavailability for mangos. In conclusion, the film prepared via Pickering emulsion showed satisfactory properties which had great potential in fruit preservation.
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Affiliation(s)
- Yiqin Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, PR China
| | - Yijing Pu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, PR China
| | - Haitao Jiang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, PR China
| | - Luyao Chen
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, PR China
| | - Chaoyu Shen
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, PR China.
| | - Wanli Zhang
- College of Food Science and Engineering, Hainan University, Haikou 570228, PR China
| | - Jiankang Cao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, PR China.
| | - Weibo Jiang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, PR China.
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7
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Gambhir P, Raghuvanshi U, Kumar R, Sharma AK. Transcriptional regulation of tomato fruit ripening. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:289-303. [PMID: 38623160 PMCID: PMC11016043 DOI: 10.1007/s12298-024-01424-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 01/15/2024] [Accepted: 02/27/2024] [Indexed: 04/17/2024]
Abstract
An intrinsic and genetically determined ripening program of tomato fruits often depends upon the appropriate activation of tissue- and stage-specific transcription factors in space and time. The past two decades have yielded considerable progress in detailing these complex transcriptional as well as hormonal regulatory circuits paramount to fleshy fruit ripening. This non-linear ripening process is strongly controlled by the MADS-box and NOR family of proteins, triggering a transcriptional response associated with the progression of fruit ripening. Deepening insights into the connection between MADS-RIN and plant hormones related transcription factors, such as ERFs and ARFs, further conjugates the idea that several signaling units work in parallel to define an output fruit ripening transcriptome. Besides these TFs, the role of other families of transcription factors such as MYB, GLK, WRKY, GRAS and bHLH have also emerged as important ripening regulators. Other regulators such as EIN and EIL proteins also determine the transcriptional landscape of ripening fruits. Despite the abundant knowledge of the complex spectrum of ripening networks in the scientific domain, identifying more ripening effectors would pave the way for a better understanding of fleshy fruit ripening at the molecular level. This review provides an update on the transcriptional regulators of tomato fruit ripening.
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Affiliation(s)
- Priya Gambhir
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021 India
| | - Utkarsh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021 India
| | - Rahul Kumar
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, 500046 India
| | - Arun Kumar Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021 India
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Cao F, Guo C, Wang X, Wang X, Yu L, Zhang H, Zhang J. Genome-wide identification, evolution, and expression analysis of the NAC gene family in chestnut ( Castanea mollissima). Front Genet 2024; 15:1337578. [PMID: 38333622 PMCID: PMC10850246 DOI: 10.3389/fgene.2024.1337578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/18/2024] [Indexed: 02/10/2024] Open
Abstract
The NAC gene family is one of the most important transcription factor families specific to plants, responsible for regulating many biological processes, including development, stress response, and signal transduction. However, it has not yet been characterized in chestnut, an important nut tree species. Here, we identified 115 CmNAC genes in the chestnut genome, which were divided into 16 subgroups based on the phylogenetic analysis. Numerous cis-acting elements related to auxin, gibberellin, and abscisic acid were identified in the promoter region of CmNACs, suggesting that they play an important role in the growth and development of chestnut. The results of the collinear analysis indicated that dispersed duplication and whole-genome-duplication were the main drivers of CmNAC gene expansion. RNA-seq data of developmental stages of chestnut nut, bud, and ovule revealed the expression patterns of CmNAC genes. Additionally, qRT-PCR experiments were used to verify the expression levels of some CmNAC genes. The comprehensive analysis of the above results revealed that some CmNAC members may be related to chestnut bud and nut development, as well as ovule fertility. The systematic analysis of this study will help to increase understanding of the potential functions of the CmNAC genes in chestnut growth and development.
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Affiliation(s)
- Fei Cao
- College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
- Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Chunlei Guo
- College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
- Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Xiangyu Wang
- The Office of Scientific Research, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Xuan Wang
- College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
- Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Liyang Yu
- College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
- Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Haie Zhang
- College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
- Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Jingzheng Zhang
- College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
- Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
- Hebei Collaborative Innovation Center of Chestnut Industry, Qinhuangdao, Hebei, China
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9
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Ding Z, Yao Y, Yao K, Hou X, Zhang Z, Huang Y, Wang C, Liao W. SlSERK3B Promotes Tomato Seedling Growth and Development by Regulating Photosynthetic Capacity. Int J Mol Sci 2024; 25:1336. [PMID: 38279340 PMCID: PMC10816166 DOI: 10.3390/ijms25021336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 01/18/2024] [Accepted: 01/20/2024] [Indexed: 01/28/2024] Open
Abstract
Brassinosteroids (BRs) are a group of polyhydroxylated steroids for plant growth and development, regulating numerous physiological and biochemical processes and participating in multi-pathway signaling in plants. 24-Epibrassinolide (EBR) is the most commonly used BR for the investigation of the effects of exogenous steroidal phytohormones on plant physiology. Although SlSERK3B is considered a gene involved in the brassinosteroid (BR) signaling pathway, its specific role in plant growth and development has not been reported in detail. In this study, tomato (Solanum lycopersicum L.) seedlings treated with 0.05 μmol L-1 EBR showed a significant increase in plant height, stem diameter, and fresh weight, demonstrating that BR promotes the growth of tomato seedlings. EBR treatment increased the expression of the BR receptor gene SlBRI1, the co-receptor gene SlSERK3A and its homologs SlSERK3B, and SlBZR1. The SlSERK3B gene was silenced by TRV-mediated virus-induced gene silencing (VIGS) technology. The results showed that both brassinolide (BL) content and BR synthesis genes were significantly up-regulated in TRV-SlSERK3B-infected seedlings compared to the control seedlings. In contrast, plant height, stem diameter, fresh weight, leaf area and total root length were significantly reduced in silenced plants. These results suggest that silencing SlSERK3B may affect BR synthesis and signaling, thereby affecting the growth of tomato seedlings. Furthermore, the photosynthetic capacity of TRV-SlSERK3B-infected tomato seedlings was reduced, accompanied by decreased photosynthetic pigment content chlorophyll fluorescence, and photosynthesis parameters. The expression levels of chlorophyll-degrading genes were significantly up-regulated, and carotenoid-synthesising genes were significantly down-regulated in TRV-SlSERK3B-infected seedlings. In conclusion, silencing of SlSERK3B inhibited BR signaling and reduced photosynthesis in tomato seedlings, and this correlation suggests that SlSERK3B may be related to BR signaling and photosynthesis enhancement.
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Affiliation(s)
| | | | | | | | | | | | | | - Weibiao Liao
- College of Horticulture, Gansu Agricultural University, 1 Yinmen Village, Anning District, Lanzhou 730070, China; (Z.D.); (Y.Y.); (K.Y.); (X.H.); (Z.Z.); (Y.H.); (C.W.)
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10
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Baranov D, Timerbaev V. Recent Advances in Studying the Regulation of Fruit Ripening in Tomato Using Genetic Engineering Approaches. Int J Mol Sci 2024; 25:760. [PMID: 38255834 PMCID: PMC10815249 DOI: 10.3390/ijms25020760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/28/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024] Open
Abstract
Tomato (Solanum lycopersicum L.) is one of the most commercially essential vegetable crops cultivated worldwide. In addition to the nutritional value, tomato is an excellent model for studying climacteric fruits' ripening processes. Despite this, the available natural pool of genes that allows expanding phenotypic diversity is limited, and the difficulties of crossing using classical selection methods when stacking traits increase proportionally with each additional feature. Modern methods of the genetic engineering of tomatoes have extensive potential applications, such as enhancing the expression of existing gene(s), integrating artificial and heterologous gene(s), pointing changes in target gene sequences while keeping allelic combinations characteristic of successful commercial varieties, and many others. However, it is necessary to understand the fundamental principles of the gene molecular regulation involved in tomato fruit ripening for its successful use in creating new varieties. Although the candidate genes mediate ripening have been identified, a complete picture of their relationship has yet to be formed. This review summarizes the latest (2017-2023) achievements related to studying the ripening processes of tomato fruits. This work attempts to systematize the results of various research articles and display the interaction pattern of genes regulating the process of tomato fruit ripening.
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Affiliation(s)
- Denis Baranov
- Laboratory of Expression Systems and Plant Genome Modification, Branch of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 142290 Pushchino, Russia;
- Laboratory of Plant Genetic Engineering, All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
| | - Vadim Timerbaev
- Laboratory of Expression Systems and Plant Genome Modification, Branch of Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, 142290 Pushchino, Russia;
- Laboratory of Plant Genetic Engineering, All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia
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11
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Kurowska M, Daszkowska-Golec A. Molecular mechanisms of SNAC1 (Stress-responsive NAC1) in conferring the abiotic stress tolerance. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 337:111894. [PMID: 37813193 DOI: 10.1016/j.plantsci.2023.111894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 10/06/2023] [Accepted: 10/06/2023] [Indexed: 10/11/2023]
Abstract
NAC family gene - SNAC1 (Stress-responsive NAC1) is responsive to drought, salt, cold stress, and ABA. It acts as a regulator in mediating tolerance to abiotic stress through different pathways. Abiotic stress, among them drought and salinity, are adverse factors for plant growth and crop productivity. SNAC1 was an object of high interest according to the effect of improved drought and salt tolerance when overexpressed in different plant species such as rice, wheat, barley, cotton, maize, banana, or oat. SNAC1 functions by regulating the expression of genes that contain the NAC Recognized Sequence (NACRS) within their promoter region. This gene is induced by drought, specifically in guard cells. Its downstream targets have been identified. The role of SNAC1 in molecular and physiological responses during abiotic stress has been proposed, but this knowledge still needs to be expanded. Here, we describe recent advances in understanding the action of SNAC1 in adapting plants to abiotic stress.
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Affiliation(s)
- Marzena Kurowska
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellońska 28, 40-032 Katowice, Poland.
| | - Agata Daszkowska-Golec
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellońska 28, 40-032 Katowice, Poland
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Han K, Zhao Y, Sun Y, Li Y. NACs, generalist in plant life. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2433-2457. [PMID: 37623750 PMCID: PMC10651149 DOI: 10.1111/pbi.14161] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 07/24/2023] [Accepted: 08/01/2023] [Indexed: 08/26/2023]
Abstract
Plant-specific NAC proteins constitute a major transcription factor family that is well-known for its roles in plant growth, development, and responses to abiotic and biotic stresses. In recent years, there has been significant progress in understanding the functions of NAC proteins. NAC proteins have a highly conserved DNA-binding domain; however, their functions are diverse. Previous understanding of the structure of NAC transcription factors can be used as the basis for their functional diversity. NAC transcription factors consist of a target-binding domain at the N-terminus and a highly versatile C-terminal domain that interacts with other proteins. A growing body of research on NAC transcription factors helps us comprehend the intricate signalling network and transcriptional reprogramming facilitated by NAC-mediated complexes. However, most studies of NAC proteins have been limited to a single function. Here, we discuss the upstream regulators, regulatory components and targets of NAC in the context of their prospective roles in plant improvement strategies via biotechnology intervention, highlighting the importance of the NAC transcription factor family in plants and the need for further research.
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Affiliation(s)
- Kunjin Han
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Ye Zhao
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Yuhan Sun
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Yun Li
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
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Wei W, Yang YY, Chen JY, Lakshmanan P, Kuang JF, Lu WJ, Shan W. MaNAC029 modulates ethylene biosynthesis and fruit quality and undergoes MaXB3-mediated proteasomal degradation during banana ripening. J Adv Res 2023; 53:33-47. [PMID: 36529351 PMCID: PMC10658243 DOI: 10.1016/j.jare.2022.12.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 10/12/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
INTRODUCTIONS Ethylene regulates ripening by activating various metabolic pathways that controlcolor, aroma, flavor, texture, and consequently, the quality of fruits. However, the modulation of ethylene biosynthesis and quality formation during banana fruit ripening remains unclear. OBJECTIVES The present study aimed to identify the regulatory module that regulates ethylene and fruit quality-related metabolisms during banana fruit ripening. METHODS We used RNA-seq to compare unripe and ripe banana fruits and identified a ripening-induced NAC transcription factor, MaNAC029. We further performed DNA affinity purification sequencing to identify the MaNAC029's target genes involved in ethylene biosynthesis and fruit quality formation, and electrophoretic mobility shift assay, chromatin immunoprecipitation with real-time polymerase chain reaction and dual luciferase assays to explore the underlying regulatory mechanisms. Immunoprecipitation combined with mass spectrometry, yeast two-hybrid assay, and bimolecular fluorescence complementation assay were used to screen and verify the proteins interacting with MaNAC029. Finally, the function of MaNAC029 and its interacting protein associated with ethylene biosynthesis and quality formation was verified through transient overexpression experiments in banana fruits. RESULTS The study identified a nucleus-localized, ripening-induced NAC transcription factor MaNAC029. It transcriptionally activated genes associated with ethylene biosynthesis and a variety of cellular metabolisms related to fruit quality formation (cell wall degradation, starch degradation, aroma compound synthesis, and chlorophyll catabolism) by directly modulating their promoter activity during ripening. Overexpression of MaNAC029 in banana fruits activated ethylene biosynthesis and accelerated fruit ripening and quality formation. Notably, the E3 ligase MaXB3 interacted with and ubiquitinated MaNAC029 protein, facilitating MaNAC029 proteasomal degradation. Consistent with this finding, MaXB3 overexpression attenuated MaNAC029-enhanced ethylene biosynthesis and quality formation. CONCLUSION Our findings demonstrate that a MaXB3-MaNAC029 module regulates ethylene biosynthesis and a series of cellular metabolisms related to fruit quality formation during banana ripening. These results expand the understanding of the transcriptional and post-translational mechanisms of fruit ripening and quality formation.
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Affiliation(s)
- Wei Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Ying-Ying Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Jian-Ye Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Prakash Lakshmanan
- Sugarcane Research Institute, Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture/Guangxi Key Laboratory of Sugarcane Genetic Improvement, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin, Southwest University, Chongqing 400716, China; Queensland Alliance for Agriculture and Food Innovation, University of Queensland, St Lucia 4067, QLD, Australia
| | - Jian-Fei Kuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Wang-Jin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Wei Shan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China.
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Fu M, Li F, Zhou S, Guo P, Chen Y, Xie Q, Chen G, Hu Z. Trihelix transcription factor SlGT31 regulates fruit ripening mediated by ethylene in tomato. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5709-5721. [PMID: 37527459 DOI: 10.1093/jxb/erad300] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 07/31/2023] [Indexed: 08/03/2023]
Abstract
Trihelix proteins are plant-specific transcription factors that are classified as GT factors due to their binding specificity for GT elements, and they play crucial roles in development and stress responses. However, their involvement in fruit ripening and transcriptional regulatory mechanisms remains largely unclear. In this study, we cloned SlGT31, encoding a trihelix protein in tomato (Solanum lycopersicum), and determined that its relative expression was significantly induced by the application of exogenous ethylene whereas it was repressed by the ethylene-inhibitor 1-methylcyclopropene. Suppression of SlGT31 expression resulted in delayed fruit ripening, decreased accumulation of total carotenoids, and reduced ethylene content, together with inhibition of expression of genes related to ethylene and fruit ripening. Conversely, SlGT31-overexpression lines showed opposite results. Yeast one-hybrid and dual-luciferase assays indicated that SlGT31 can bind to the promoters of two key ethylene-biosynthesis genes, ACO1 and ACS4. Taken together, our results indicate that SlGT31 might act as a positive modulator during fruit ripening.
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Affiliation(s)
- Mengjie Fu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China
| | - Fenfen Li
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China
| | - Shengen Zhou
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China
| | - Pengyu Guo
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China
| | - Yanan Chen
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China
| | - Qiaoli Xie
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China
| | - Guoping Chen
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China
| | - Zongli Hu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China
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Tiwari JK, Singh AK, Behera TK. CRISPR/Cas genome editing in tomato improvement: Advances and applications. FRONTIERS IN PLANT SCIENCE 2023; 14:1121209. [PMID: 36909403 PMCID: PMC9995852 DOI: 10.3389/fpls.2023.1121209] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 02/02/2023] [Indexed: 06/12/2023]
Abstract
The narrow genetic base of tomato poses serious challenges in breeding. Hence, with the advent of clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein9 (CRISPR/Cas9) genome editing, fast and efficient breeding has become possible in tomato breeding. Many traits have been edited and functionally characterized using CRISPR/Cas9 in tomato such as plant architecture and flower characters (e.g. leaf, stem, flower, male sterility, fruit, parthenocarpy), fruit ripening, quality and nutrition (e.g., lycopene, carotenoid, GABA, TSS, anthocyanin, shelf-life), disease resistance (e.g. TYLCV, powdery mildew, late blight), abiotic stress tolerance (e.g. heat, drought, salinity), C-N metabolism, and herbicide resistance. CRISPR/Cas9 has been proven in introgression of de novo domestication of elite traits from wild relatives to the cultivated tomato and vice versa. Innovations in CRISPR/Cas allow the use of online tools for single guide RNA design and multiplexing, cloning (e.g. Golden Gate cloning, GoldenBraid, and BioBrick technology), robust CRISPR/Cas constructs, efficient transformation protocols such as Agrobacterium, and DNA-free protoplast method for Cas9-gRNAs ribonucleoproteins (RNPs) complex, Cas9 variants like PAM-free Cas12a, and Cas9-NG/XNG-Cas9, homologous recombination (HR)-based gene knock-in (HKI) by geminivirus replicon, and base/prime editing (Target-AID technology). This mini-review highlights the current research advances in CRISPR/Cas for fast and efficient breeding of tomato.
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Affiliation(s)
- Jagesh Kumar Tiwari
- Division of Vegetable Improvement, Indian Council of Agricultural Research-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Anand Kumar Singh
- Division of Horticulture, Indian Council of Agricultural Research, Krishi Anusandhan Bhawan - II, Pusa, New Delhi, India
| | - Tusar Kanti Behera
- Division of Vegetable Improvement, Indian Council of Agricultural Research-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
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Liu J, Qiao Y, Li C, Hou B. The NAC transcription factors play core roles in flowering and ripening fundamental to fruit yield and quality. FRONTIERS IN PLANT SCIENCE 2023; 14:1095967. [PMID: 36909440 PMCID: PMC9996081 DOI: 10.3389/fpls.2023.1095967] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
Fruits are derived from flowers and play an important role in human food, nutrition, and health. In general, flowers determine the crop yield, and ripening affects the fruit quality. Although transcription factors (TFs) only account for a small part of plant transcriptomes, they control the global gene expression and regulation. The plant-specific NAC (NAM, ATAF, and CUC) TFs constitute a large family evolving concurrently with the transition of both aquatic-to-terrestrial plants and vegetative-to-reproductive growth. Thus, NACs play an important role in fruit yield and quality by determining shoot apical meristem (SAM) inflorescence and controlling ripening. The present review focuses on the various properties of NACs together with their function and regulation in flower formation and fruit ripening. Hitherto, we have a better understanding of the molecular mechanisms of NACs in ripening through abscisic acid (ABA) and ethylene (ETH), but how NACs regulate the expression of the inflorescence formation-related genes is largely unknown. In the future, we should focus on the analysis of NAC redundancy and identify the pivotal regulators of flowering and ripening. NACs are potentially vital manipulation targets for improving fruit quantity and quality.
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Affiliation(s)
- Jianfeng Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuyuan Qiao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cui Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bingzhu Hou
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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Manosalva Pérez N, Vandepoele K. Prediction of Transcription Factor Regulators and Gene Regulatory Networks in Tomato Using Binding Site Information. Methods Mol Biol 2023; 2698:323-349. [PMID: 37682483 DOI: 10.1007/978-1-0716-3354-0_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Gene regulatory networks (GRNs) represent the regulatory links between transcription factors (TF) and their target genes. In plants, they are essential to understand transcriptional programs that control important agricultural traits such as yield or (a)biotic stress response. Although several high- and low-throughput experimental methods have been developed to map GRNs in plants, these are sometimes expensive, come with laborious protocols, and are not always optimized for tomato, one of the most important horticultural crops worldwide. In this chapter, we present a computational method that covers two protocols: one protocol to map gene identifiers between two different tomato genome assemblies, and another protocol to predict putative regulators and delineate GRNs given a set of functionally related or coregulated genes by exploiting publicly available TF-binding information. As an example, we applied the motif enrichment protocol on tomato using upregulated genes in response to jasmonate, as well as upregulated and downregulated genes in plants with genotypes OENAM1 and nam1, respectively. We found that our protocol accurately infers the expected TFs as top enriched regulators and identifies GRNs functionally enriched in biological processes related with the experimental context under study.
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Affiliation(s)
- Nicolás Manosalva Pérez
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- Center for Plant Systems Biology, VIB, Ghent, Belgium.
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium.
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Integrated Analysis of Widely Targeted Metabolomics and Transcriptomics Reveals the Effects of Transcription Factor NOR-like1 on Alkaloids, Phenolic Acids, and Flavonoids in Tomato at Different Ripening Stages. Metabolites 2022; 12:metabo12121296. [PMID: 36557334 PMCID: PMC9853326 DOI: 10.3390/metabo12121296] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/14/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Tomato is abundant in alkaloids, phenolic acids, and flavonoids; however, the effect of transcription factor NOR-like1 on these metabolites in tomato is unclear. We used a combination of widely targeted metabolomics and transcriptomics to analyze wild-type tomatoes and CR-NOR-like1 tomatoes. A total of 83 alkaloids, 85 phenolic acids, and 96 flavonoids were detected with significant changes. Combined with a KEGG enrichment analysis, we revealed 16 differentially expressed genes (DEGs) in alkaloid-related arginine and proline metabolism, 60 DEGs were identified in the phenolic acid-related phenylpropane biosynthesis, and 30 DEGs were identified in the flavonoid-related biosynthesis pathway. In addition, some highly correlated differential-expression genes with differential metabolites were further identified by correlation analysis. The present research provides a preliminary view of the effects of NOR-like1 transcription factor on alkaloid, phenolic acid, and flavonoid accumulation in tomatoes at different ripening stages based on widely targeted metabolomics and transcriptomics in plants, laying the foundation for extending fruit longevity and shelf life as well as cultivating stress-resistant plants.
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Qi X, Dong Y, Liu C, Song L, Chen L, Li M. The PavNAC56 transcription factor positively regulates fruit ripening and softening in sweet cherry (Prunus avium). PHYSIOLOGIA PLANTARUM 2022; 174:e13834. [PMID: 36437693 DOI: 10.1111/ppl.13834] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/11/2022] [Accepted: 11/24/2022] [Indexed: 06/16/2023]
Abstract
The rapid softening of sweet cherry fruits during ripening results in the deterioration of fruit quality. However, few genes related to sweet cherry fruit ripening and softening have been identified, and the molecular regulatory mechanisms underlying this process are poorly understood. Here, we identified and functionally characterized PavNAC56, a NAC transcription factor that positively regulates sweet cherry fruit ripening and softening. Gene expression analyses showed that PavNAC56 was specifically and abundantly expressed in the fruit, and its transcript levels increased in response to abscisic acid (ABA). A subcellular localization analysis revealed that PavNAC56 is a nucleus-localized protein. Virus-induced gene silencing of PavNAC56 inhibited fruit ripening, enhanced fruit firmness, decreased the contents of ABA, anthocyanins, and soluble solids, and down-regulated several fruit ripening-related genes. Yeast one-hybrid and dual-luciferase assays showed that PavNAC56 directly binds to the promoters of several genes related to cell wall metabolism (PavPG2, PavEXPA4, PavPL18, and PavCEL8) and activates their expression. Overall, our findings show that PavNAC56 plays an indispensable role in controlling the ripening and softening of sweet cherry fruit and provides new insights into the regulatory mechanisms by which NAC transcription factors affect nonclimacteric fruit ripening and softening.
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Affiliation(s)
- Xiliang Qi
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Yuanxin Dong
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Congli Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Lulu Song
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Lei Chen
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Ming Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
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Huang W, Hu N, Xiao Z, Qiu Y, Yang Y, Yang J, Mao X, Wang Y, Li Z, Guo H. A molecular framework of ethylene-mediated fruit growth and ripening processes in tomato. THE PLANT CELL 2022; 34:3280-3300. [PMID: 35604102 PMCID: PMC9421474 DOI: 10.1093/plcell/koac146] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/22/2022] [Indexed: 05/08/2023]
Abstract
Although the role of ethylene in tomato (Solanum lycopersicum) fruit ripening has been intensively studied, its role in tomato fruit growth remains poorly understood. In addition, the relationship between ethylene and the developmental factors NON-RIPENING (NOR) and RIPENING INHIBITOR (RIN) during ripening is under debate. Here, we carried out comprehensive genetic analyses of genome-edited mutants of tomato ETHYLENE INSENSITIVE 2 (SlEIN2), four EIN3-like genes (SlEIL1-4), and three EIN3 BINDING F-box protein genes (SlEBF1-3). Both slein2-1 and the high-order sleil mutant (sleil1 sleil2 sleil3/SlEIL3 sleil4) showed reduced fruit size, mainly due to decreased auxin biosynthesis. During fruit maturation, slein2 mutants displayed the complete cessation of ripening, which was partially rescued by slebf1 but not slebf2 or slebf3. We also discovered that ethylene directly activates the expression of the developmental genes NOR, RIN, and FRUITFULL1 (FUL1) via SlEIL proteins. Indeed, overexpressing these genes partially rescued the ripening defects of slein2-1. Finally, the signal intensity of the ethylene burst during fruit maturation was intimately connected with the progression of full ripeness. Collectively, our work uncovers a critical role of ethylene in fruit growth and supports a molecular framework of ripening control in which the developmental factors NOR, RIN, and FUL1 act downstream of ethylene signaling.
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Affiliation(s)
- Wei Huang
- Department of Biology,Institute of Plant and Food Science, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
| | - Nan Hu
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Zhina Xiao
- Department of Biology,Institute of Plant and Food Science, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
| | - Yuping Qiu
- Department of Biology,Institute of Plant and Food Science, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
| | - Yan Yang
- Department of Biology,Institute of Plant and Food Science, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
| | - Jie Yang
- Department of Biology,Institute of Plant and Food Science, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
| | - Xin Mao
- Department of Biology,Institute of Plant and Food Science, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
| | - Yichuan Wang
- Department of Biology,Institute of Plant and Food Science, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
| | - Zhengguo Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China
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Liu GS, Li HL, Grierson D, Fu DQ. NAC Transcription Factor Family Regulation of Fruit Ripening and Quality: A Review. Cells 2022; 11:cells11030525. [PMID: 35159333 PMCID: PMC8834055 DOI: 10.3390/cells11030525] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/27/2022] [Accepted: 01/31/2022] [Indexed: 01/18/2023] Open
Abstract
The NAC transcription factor (TF) family is one of the largest plant-specific TF families and its members are involved in the regulation of many vital biological processes during plant growth and development. Recent studies have found that NAC TFs play important roles during the ripening of fleshy fruits and the development of quality attributes. This review focuses on the advances in our understanding of the function of NAC TFs in different fruits and their involvement in the biosynthesis and signal transduction of plant hormones, fruit textural changes, color transformation, accumulation of flavor compounds, seed development and fruit senescence. We discuss the theoretical basis and potential regulatory models for NAC TFs action and provide a comprehensive view of their multiple roles in modulating different aspects of fruit ripening and quality.
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Affiliation(s)
- Gang-Shuai Liu
- Laboratory of Fruit Biology, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China; (G.-S.L.); (H.-L.L.)
| | - Hong-Li Li
- Laboratory of Fruit Biology, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China; (G.-S.L.); (H.-L.L.)
| | - Donald Grierson
- Laboratory of Fruit Quality Biology, Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China;
- Plant Sciences Division, School of Biosciences, Sutton Bonington Campus, University of Nottingham, Loughborough LE12 5RD, UK
| | - Da-Qi Fu
- Laboratory of Fruit Biology, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China; (G.-S.L.); (H.-L.L.)
- Correspondence:
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