title: Integrative transcript and metabolite analysis of nutritionally enhanced DE-ETIOLATED1 downregulated tomato fruit.
abstract: Fruit-specific downregulation of the DE-ETIOLATED1 (DET1) gene product results in tomato fruits (Solanum lycopersicum) containing enhanced nutritional antioxidants, with no detrimental effects on yield. In an attempt to further our understanding of how modulation of this gene leads to improved quality traits, detailed targeted and multilevel omic characterization has been performed. Metabolite profiling revealed quantitative increases in carotenoid, tocopherol, phenylpropanoids, flavonoids, and anthocyanidins. Qualitative differences could also be identified within the phenolics, including unique formation in fruit pericarp tissues. These changes resulted in increased total antioxidant content both in the polar and nonpolar fractions. Increased transcription of key biosynthetic genes is a likely mechanism producing elevated phenolic-based metabolites. By contrast, high levels of isoprenoids do not appear to result from transcriptional regulation but are more likely related to plastid-based parameters, such as increased plastid volume per cell. Parallel metabolomic and transcriptomic analyses reveal the widespread effects of DET1 downregulation on diverse sectors of metabolism and sites of synthesis. Correlation analysis of transcripts and metabolites independently indicated strong coresponses within and between related pathways/processes. Interestingly, despite the fact that secondary metabolites were the most severely affected in ripe tomato fruit, our integrative analyses suggest that the coordinated activation of core metabolic processes in cell types amenable to plastid biogenesis is the main effect of DET1 loss of function.
authors.affiliation: Centre for Systems and Synthetic Biology, University of London, Egham, Surrey TW20 0EX, United Kingdom.
authors.forename: Eugenia M A
authors.initials: EM
authors.lastname: Enfissi
authors.forename: Fredy
authors.initials: F
authors.lastname: Barneche
authors.forename: Ikhlak
authors.initials: I
authors.lastname: Ahmed
authors.forename: Christiane
authors.initials: C
authors.lastname: Lichtlé
authors.forename: Christopher
authors.initials: C
authors.lastname: Gerrish
authors.forename: Ryan P
authors.initials: RP
authors.lastname: McQuinn
authors.forename: James J
authors.initials: JJ
authors.lastname: Giovannoni
authors.forename: Enrique
authors.initials: E
authors.lastname: Lopez-Juez
authors.forename: Chris
authors.initials: C
authors.lastname: Bowler
authors.forename: Peter M
authors.initials: PM
authors.lastname: Bramley
authors.forename: Paul D
authors.initials: PD
authors.lastname: Fraser
mesh_terms: D000975:Antioxidants / Q000032:analysis; D002338:Carotenoids / Q000032:analysis; D015536:Down-Regulation; D005419:Flavonoids / Q000032:analysis; D005638:Fruit / Q000235:genetics / Q000378:metabolism*; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D018551:Solanum lycopersicum / Q000235:genetics* / Q000378:metabolism; D055442:Metabolome; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism*; D018749:RNA, Plant / Q000235:genetics
chemical_list: D000975:Antioxidants; D005419:Flavonoids; D009687:Nuclear Proteins; D010940:Plant Proteins; D018749:RNA, Plant; D002338:Carotenoids