Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development

• Published in: The Plant journal : for cell and molecular biology Vol. 68; no. 6; pp. 999 - 1013
• Main Authors: Rohrmann, Johannes, Tohge, Takayuki, Alba, Rob, Osorio, Sonia, Caldana, Camila, McQuinn, Ryan, Arvidsson, Samuel, van der Merwe, Margaretha J, Riaño‐Pachón, Diego Mauricio, Mueller‐Roeber, Bernd, Fei, Zhangjun, Nesi, Adriano Nunes, Giovannoni, James J, Fernie, Alisdair R
• Format: Journal Article
• Language: English
• Published: Oxford, UK Blackwell Publishing Ltd 01.12.2011; Blackwell
• Subjects: Arabidopsis; Biological and medical sciences; Cell differentiation, maturation, development, hematopoiesis; Cell physiology; complementary DNA; data collection; Development; DNA microarrays; fleshy fruit ripening; Fruit; Fruit - growth & development; fruiting; Fruits; Fundamental and applied biological sciences. Psychology; Gene Expression Profiling; Gene Expression Regulation, Plant; Gene regulation; genes; Genes, Plant; Genetic control; genetics; growth & development; Light effects; Lycopersicon esculentum; Lycopersicon esculentum - genetics; Lycopersicon esculentum - growth & development; Lycopersicon esculentum - metabolism; metabolism; Metabolites; metabolomics; microarray; microarray technology; Molecular and cellular biology; Molecular genetics; mutants; Oligonucleotide Array Sequence Analysis; pericarp; phenolic compounds; Phenols; phenotype; phototransduction; Pigments; Plant biology; Plant physiology and development; Polymerase chain reaction; quantitative RT‐PCR; Real-Time Polymerase Chain Reaction; Ripening; Secondary metabolites; Signal transduction; Solanum; Solanum lycopersicum; Tomatoes; transcription (genetics); transcription factor; Transcription factors; Transcription Factors - genetics; Transcription Factors - metabolism; Transcription. Transcription factor. Splicing. Rna processing; Shift; Metabolomics; Fruit; Transcription; Metabolite; Solanum lycopersicum; Microarray; Ripening; Regulation(control); Dicotyledones; Angiospermae; Lycopersicon esculentum; quantitative RT-PCR; Development; Spermatophyta; Solanaceae; Transcription factor; Reverse transcription polymerase chain reaction; fleshy fruit ripening
• ISSN: 0960-7412; 1365-313X; 1365-313X
• DOI: 10.1111/j.1365-313X.2011.04750.x

Maturation of fleshy fruits such as tomato (Solanum lycopersicum) is subject to tight genetic control. Here we describe the development of a quantitative real‐time PCR platform that allows accurate quantification of the expression level of approximately 1000 tomato transcription factors. In addition to utilizing this novel approach, we performed cDNA microarray analysis and metabolite profiling of primary and secondary metabolites using GC‐MS and LC‐MS, respectively. We applied these platforms to pericarp material harvested throughout fruit development, studying both wild‐type Solanum lycopersicum cv. Ailsa Craig and the hp1 mutant. This mutant is functionally deficient in the tomato homologue of the negative regulator of the light signal transduction gene DDB1 from Arabidopsis, and is furthermore characterized by dramatically increased pigment and phenolic contents. We choose this particular mutant as it had previously been shown to have dramatic alterations in the content of several important fruit metabolites but relatively little impact on other ripening phenotypes. The combined dataset was mined in order to identify metabolites that were under the control of these transcription factors, and, where possible, the respective transcriptional regulation underlying this control. The results are discussed in terms of both programmed fruit ripening and development and the transcriptional and metabolic shifts that occur in parallel during these processes.