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Shi Y, Hu G, Wang Y, Liang Q, Su D, Lu W, Deng W, Bouzayen M, Liu Y, Li Z, Huang B. The SlGRAS9-SlZHD17 transcriptional cascade regulates chlorophyll and carbohydrate metabolism contributing to fruit quality traits in tomato. THE NEW PHYTOLOGIST 2024; 241:2540-2557. [PMID: 38263687 DOI: 10.1111/nph.19530] [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: 07/28/2023] [Accepted: 12/12/2023] [Indexed: 01/25/2024]
Abstract
Some essential components of fleshy fruits are dependent on photosynthetic activity and carbohydrate metabolism. Nevertheless, the regulatory mechanisms linking chlorophyll and carbohydrate metabolism remain partially understood. Here, we uncovered the role of SlGRAS9 and SlZHD17 transcription factors in controlling chlorophyll and carbohydrate accumulation in tomato fruit. Knockout or knockdown of SlGRAS9 or SlZHD17 resulted in marked increase in chlorophyll content, reprogrammed chloroplast biogenesis and enhanced accumulation of starch and soluble sugars. Combined genome-wide transcriptomic profiling and promoter-binding experiments unveiled a complex mechanism in which the SlGRAS9/SlZHD17 regulatory module modulates the expression of chloroplast and sugar metabolism either via a sequential transcriptional cascade or through binding of both TFs to the same gene promoters, or, alternatively, via parallel pathways where each of the TFs act on different target genes. For instance, the regulation of SlAGPaseS1 and SlSUS1 is mediated by SlZHD17 whereas that of SlVI and SlGLK1 occurs only through SlGRAS9 without the intervention of SlZHD17. Both SlGRAS9 and SlZHD17 can also directly bind the promoter of SlPOR-B to regulate its expression. Taken together, our findings uncover two important regulators acting synergistically to manipulate chlorophyll and carbohydrate accumulation and provide new potential breeding targets for improving fruit quality in fleshy fruits.
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Affiliation(s)
- Yuan Shi
- Key Laboratory of Plant Hormones and Molecular Breeding of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Guojian Hu
- Key Laboratory of Plant Hormones and Molecular Breeding of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
- Laboratoire de Recherche en Sciences Vegetales - Genomique et Biotechnologie des Fruits - UMR5546, Universite de Toulouse, CNRS, UPS, Toulouse-INP, Toulouse, 31326, France
| | - Yan Wang
- Key Laboratory of Plant Hormones and Molecular Breeding of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Qin Liang
- Key Laboratory of Plant Hormones and Molecular Breeding of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Deding Su
- Key Laboratory of Plant Hormones and Molecular Breeding of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Wang Lu
- Key Laboratory of Plant Hormones and Molecular Breeding of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Wei Deng
- Key Laboratory of Plant Hormones and Molecular Breeding of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Mondher Bouzayen
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
- Laboratoire de Recherche en Sciences Vegetales - Genomique et Biotechnologie des Fruits - UMR5546, Universite de Toulouse, CNRS, UPS, Toulouse-INP, Toulouse, 31326, France
| | - Yudong Liu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Zhengguo Li
- Key Laboratory of Plant Hormones and Molecular Breeding of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Baowen Huang
- Key Laboratory of Plant Hormones and Molecular Breeding of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
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Ye J, Li W, Ai G, Li C, Liu G, Chen W, Wang B, Wang W, Lu Y, Zhang J, Li H, Ouyang B, Zhang H, Fei Z, Giovannoni JJ, Ye Z, Zhang Y. Genome-wide association analysis identifies a natural variation in basic helix-loop-helix transcription factor regulating ascorbate biosynthesis via D-mannose/L-galactose pathway in tomato. PLoS Genet 2019; 15:e1008149. [PMID: 31067226 PMCID: PMC6527244 DOI: 10.1371/journal.pgen.1008149] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 05/20/2019] [Accepted: 04/23/2019] [Indexed: 02/02/2023] Open
Abstract
Tomato (Solanum lycopersicum) is one of the highest-value vegetable crops worldwide. Understanding the genetic regulation of primary metabolite levels can inform efforts aimed toward improving the nutrition of commercial tomato cultivars, while maintaining key traits such as yield and stress tolerance. We identified 388 suggestive association loci (including 126 significant loci) for 92 metabolic traits including nutrition and flavor-related loci by genome-wide association study from 302 accessions in two different environments. Among them, an ascorbate quantitative trait locus TFA9 (TOMATOFRUITASCORBATEON CHROMOSOME9) co-localized with SlbHLH59, which promotes high ascorbate accumulation by directly binding to the promoter of structural genes involved in the D-mannose/L-galactose pathway. The causal mutation of TFA9 is an 8-bp InDel, named InDel_8, located in the promoter region of SlbHLH59 and spanned a 5’UTR Py-rich stretch motif affecting its expression. Phylogenetic analysis revealed that differentially expressed SlbHLH59 alleles were selected during tomato domestication. Our results provide a dramatic illustration of how ascorbate biosynthesis can be regulated and was selected during the domestication of tomato. Furthermore, the findings provide novel genetic insights into natural variation of metabolites in tomato fruit, and will promote efficient utilization of metabolite traits in tomato improvement. Deciphering the diverse, interconnected plant metabolome can facilitate crop improvement. In this study, the use of a combination of multiple technologies has allowed us to obtain novel functional and genetic insights into our GWAS investigating variation in ascorbate accumulation in tomato. The InDel_8 in the promoter of SlbHLH59 was selected during tomato domestication and determines fruit ascorbate content by directly regulating the expression of structural genes involved in ascorbate biosynthesis in tomato fruit. The genes and polymorphisms responsible for the variations identified in this study lay the foundation for further comparative genomic studies and for improving nutrition quality in tomato and other fruit crops.
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Affiliation(s)
- Jie Ye
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China.,Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, United States of America
| | - Wangfang Li
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Guo Ai
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Changxing Li
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Genzhong Liu
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Weifang Chen
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Bing Wang
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Wenqian Wang
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Yongen Lu
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Junhong Zhang
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Hanxia Li
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Bo Ouyang
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Hongyan Zhang
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, United States of America
| | - James J Giovannoni
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, New York, United States of America.,Robert W. Holley Center, US Department of Agriculture-Agricultural Research Service, Ithaca, New York, United States of America
| | - Zhibiao Ye
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Yuyang Zhang
- The Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
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Colombié S, Nazaret C, Bénard C, Biais B, Mengin V, Solé M, Fouillen L, Dieuaide-Noubhani M, Mazat JP, Beauvoit B, Gibon Y. Modelling central metabolic fluxes by constraint-based optimization reveals metabolic reprogramming of developing Solanum lycopersicum (tomato) fruit. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:24-39. [PMID: 25279440 PMCID: PMC4309433 DOI: 10.1111/tpj.12685] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 09/19/2014] [Accepted: 09/19/2014] [Indexed: 05/18/2023]
Abstract
Modelling of metabolic networks is a powerful tool to analyse the behaviour of developing plant organs, including fruits. Guided by our current understanding of heterotrophic metabolism of plant cells, a medium-scale stoichiometric model, including the balance of co-factors and energy, was constructed in order to describe metabolic shifts that occur through the nine sequential stages of Solanum lycopersicum (tomato) fruit development. The measured concentrations of the main biomass components and the accumulated metabolites in the pericarp, determined at each stage, were fitted in order to calculate, by derivation, the corresponding external fluxes. They were used as constraints to solve the model by minimizing the internal fluxes. The distribution of the calculated fluxes of central metabolism were then analysed and compared with known metabolic behaviours. For instance, the partition of the main metabolic pathways (glycolysis, pentose phosphate pathway, etc.) was relevant throughout fruit development. We also predicted a valid import of carbon and nitrogen by the fruit, as well as a consistent CO2 release. Interestingly, the energetic balance indicates that excess ATP is dissipated just before the onset of ripening, supporting the concept of the climacteric crisis. Finally, the apparent contradiction between calculated fluxes with low values compared with measured enzyme capacities suggest a complex reprogramming of the metabolic machinery during fruit development. With a powerful set of experimental data and an accurate definition of the metabolic system, this work provides important insight into the metabolic and physiological requirements of the developing tomato fruits.
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Affiliation(s)
- Sophie Colombié
- INRAUMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, F-33883, France
- *For correspondence (e-mail )
| | - Christine Nazaret
- Institut de Mathématiques de Bordeaux, ENSTBB-Institut Polytechnique de Bordeaux351 Cours de la Liberation, Talence, F-33400, France
| | - Camille Bénard
- INRAUMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, F-33883, France
| | - Benoît Biais
- INRAUMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, F-33883, France
| | - Virginie Mengin
- INRAUMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, F-33883, France
| | - Marion Solé
- INRAUMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, F-33883, France
| | - Laëtitia Fouillen
- CNRS, UMR 5200Laboratoire de Biogenèse Membranaire, Villenave D'Ornon, F-33883, France
- Univ. Bordeaux146 rue Léo-Saignat, Bordeaux Cedex, F-33076, France
| | - Martine Dieuaide-Noubhani
- INRAUMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, F-33883, France
- Univ. Bordeaux146 rue Léo-Saignat, Bordeaux Cedex, F-33076, France
| | - Jean-Pierre Mazat
- Univ. Bordeaux146 rue Léo-Saignat, Bordeaux Cedex, F-33076, France
- IBGC-CNRS1 rue Camille Saint-Saëns, Bordeaux Cedex, F-33077, France
| | - Bertrand Beauvoit
- INRAUMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, F-33883, France
- Univ. Bordeaux146 rue Léo-Saignat, Bordeaux Cedex, F-33076, France
| | - Yves Gibon
- INRAUMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, F-33883, France
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