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

Yang, Xinyu; Zhao, Xiaodan; Fu, Daqi; Zhao, Ying

doi:10.3390/metabo12121296

Cited by 9 publications

(15 citation statements)

References 48 publications

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“…Chalcone isomerase is the next limiting step in flavonoid biosynthesis that isomerize naringenin chalcone to naringenin. Similar to previous reports, CHI was negatively correlated with naringenin chalcone ( Yang et al., 2022 ). The following steps proceeding towards flavonones and anthocyanins were up-regulated in SSL (at the transcript level), whereas the steps towards quercetin, kaempferol, and eriodictyol were induced in LSL (at the metabolite level), respectively, suggesting the different pathway reprogramming in the two genotypes.…”

Section: Discussionsupporting

confidence: 91%

A metabolome and transcriptome survey to tap the dynamics of fruit prolonged shelf-life and improved quality within Greek tomato germplasm

Mellidou,

Koukounaras,

Frusciante

et al. 2023

Front. Plant Sci.

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IntroductionTomato is a high economic value crop worldwide with recognized nutritional properties and diverse postharvest potential. Nowadays, there is an emerging awareness about the exploitation and utilization of underutilized traditional germplasm in modern breeding programs. In this context, the existing diversity among Greek accessions in terms of their postharvest life and nutritional value remains largely unexplored.MethodsHerein, a detailed evaluation of 130 tomato Greek accessions for postharvest and nutritional characteristics was performed, using metabolomics and transcriptomics, leading to the selection of accessions with these interesting traits. ResultsThe results showed remarkable differences among tomato Greek accessions for overall ripening parameters (color, firmness) and weight loss. On the basis of their postharvest performance, a balance between short shelf life (SSL) and long shelf life (LSL) accessions was revealed. Metabolome analysis performed on 14 selected accessions with contrasting shelf-life potential identified a total of 206 phytonutrients and volatile compounds. In turn, transcriptome analysis in fruits from the best SSL and the best LSL accessions revealed remarkable differences in the expression profiles of transcripts involved in key metabolic pathways related to fruit quality and postharvest potential. DiscussionThe pathways towards cell wall synthesis, polyamine synthesis, ABA catabolism, and steroidal alkaloids synthesis were mostly induced in the LSL accession, whereas those related to ethylene biosynthesis, cell wall degradation, isoprenoids, phenylpropanoids, ascorbic acid and aroma (TomloxC) were stimulated in the SSL accession. Overall, these data would provide valuable insights into the molecular mechanism towards enhancing shelf-life and improving flavor and aroma of modern tomato cultivars.

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Section: Discussionsupporting

confidence: 91%

A metabolome and transcriptome survey to tap the dynamics of fruit prolonged shelf-life and improved quality within Greek tomato germplasm

Mellidou,

Koukounaras,

Frusciante

et al. 2023

Front. Plant Sci.

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“…To more precisely elucidate how these TFs affect fruit metabolite accumulation, we compared the metabolites between the WT and mutant fruit samples. The method for the targeted metabolomics analysis has been used to identify numerous metabolites in tomato (Li et al, 2020; Yang et al, 2022). The 1,052 metabolites identified in the current study were divided into 12 clusters (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Using CRISPR/Cas9 technology to target this gene resulted in the production of mutant fruit with decreased lycopene accumulation and ethylene production, but increased alkaloid contents compared with the corresponding wild-type (WT) levels. Moreover, NOR-like1 also affects phenolic acids and flavonoids (Yang et al, 2022). Although the effects of some TFs on fruit metabolism have been determined, many TFs remain uncharacterized and there is a lack of systematic research on how fruit ripening-6 Ethylene production in the fruit ripening stage was compared between the mutants and the WT (Fig.…”

Section: Introductionmentioning

confidence: 99%

Evaluation of the effects of ripening-related genes on fruit metabolites and the associated regulatory mechanisms in tomato

Jia,

Xu,

Deng

et al. 2024

Preprint

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Fruit ripening, which is a complex process involving dynamic changes to metabolites, is controlled by multiple factors, including transcription factors (TFs). Several TFs are reportedly essential regulators of tomato fruit ripening. To evaluate the effects of specific TFs on metabolite accumulation during fruit ripening, CRISPR/Cas9-mediated mutagenesis was combined with metabolome and transcriptome analyses to explore regulatory mechanisms. Specifically, we generated various genetically engineered tomato lines that differed regarding metabolite contents and fruit colors. The metabolite and transcript profiles indicated that the selected TFs have distinct functions that control fruit metabolite contents, especially carotenoids and sugars. Our findings may provide new insights into the regulatory mechanisms governing tomato fruit ripening. Moreover, a mutation toELONGATED HYPOCOTYL5(HY5) increased the tomato fruit fructose and glucose contents by approximately 20% (relative to the wild-type levels). Ourin vitroassay showed that HY5 can bind directly to the G-boxcis-element in theSWEET12cpromoter to activate expression, thereby modulating sugar transport. Our findings have clarified the mechanism regulating fruit metabolic networks, while also providing the theoretical basis for breeding horticultural crops that produce fruit with diverse flavors and colors.g

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“…UPLC-MS/MS enables the large-scale detection, along with the accurate characterization and quantification, of substances [ 25 ]. In recent years, UPLC-MS/MS-based metabolomic analysis has dominated metabolomic studies of nutrient composition and fruit quality [ 15 , 26 , 27 , 28 ]. Furthermore, explorations of metabolome and transcriptome associations have been shown to help elucidate the genetic basis of metabolic networks [ 29 ].…”

Section: Discussionmentioning

confidence: 99%

Integrative Analysis of Metabolome and Transcriptome Reveals Molecular Insight into Metabolomic Variations during Hawthorn Fruit Development

et al. 2023

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Hawthorn (Crataegus pinnatifida var. major), a cultivated fruit tree, is native and unique to China. Its fruits have high nutritional, health, and medicinal values. However, the development and ripening process of hawthorns is accompanied by dramatic changes in flavor, aroma, and bioactive phytochemicals, which are the fundamental factors that contribute to the potential health benefits and establishment of fruit quality. Therefore, an exploration of the dynamic changes in metabolites and their regulatory networks during the development of hawthorn fruits can elucidate the formation mechanisms of active substances in hawthorn fruits. In this study, we used a broad targeted metabolomics approach to identify and analyze the dynamics of metabolites in hawthorn fruits at five developmental stages. The results revealed 998 primary and secondary metabolites that were classified into 15 categories. The accumulation levels of most sugars increased during fruit development and then accelerated at the fruit ripening stage. The accumulation levels of a few organic acids (e.g., citric acid, isocitric acid, and quinic acid) continuously increased. Many organic acids exhibited significant decreasing trends. Among the 561 secondary metabolites detected, 189 were phenolic acids and 199 were flavonoids. The levels of many flavonoids were significantly reduced at later stages of fruit development; in contrast, the levels of two anthocyanins significantly increased during fruit ripening. Correlation analysis revealed that there is a certain correlation within and between primary as well as secondary metabolites during fruit development. Furthermore, the integration of metabolomic and transcriptomic data in this study revealed that changes in the expression of some differentially expressed genes (DEGs) were associated with the accumulation of metabolites such as sugars, organic acids, and flavonoids, e.g., the upregulated expression levels of CS (citrate synthase) genes were consistent with the continued accumulation of citric acid. Overall, this study demonstrates the metabolic changes that occur during the development of hawthorn fruit, explores the molecular mechanisms that underlie metabolite changes during fruit development, and lays a strong theoretical foundation for the improvement of hawthorn fruit quality and the development of functional components.

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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

Cited by 9 publications

References 48 publications

A metabolome and transcriptome survey to tap the dynamics of fruit prolonged shelf-life and improved quality within Greek tomato germplasm

A metabolome and transcriptome survey to tap the dynamics of fruit prolonged shelf-life and improved quality within Greek tomato germplasm

Evaluation of the effects of ripening-related genes on fruit metabolites and the associated regulatory mechanisms in tomato

Integrative Analysis of Metabolome and Transcriptome Reveals Molecular Insight into Metabolomic Variations during Hawthorn Fruit Development

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