First published online October 27, 2006; 10.1104/pp.106.088534
Plant Physiology 142:1380-1396 (2006)
© 2006 American Society of Plant Biologists
BIOCHEMICAL PROCESSES AND MACROMOLECULAR STRUCTURES
Integrated Analysis of Metabolite and Transcript Levels Reveals the Metabolic Shifts That Underlie Tomato Fruit Development and Highlight Regulatory Aspects of Metabolic Network Behavior1,[W]
Fernando Carrari,
Charles Baxter,
Björn Usadel,
Ewa Urbanczyk-Wochniak,
Maria-Ines Zanor,
Adriano Nunes-Nesi,
Victoria Nikiforova,
Danilo Centero,
Antje Ratzka,
Markus Pauly,
Lee J. Sweetlove and
Alisdair R. Fernie*
Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Golm-Postdam, Germany (F.C., B.U., E.U.-W., M.-I.Z., A.N.-N., V.N., D.C., A.R., M.P., A.R.F.); Instituto de Biotecnología, CICVyA, Instituto Nacional de Tecnología Agrícola Argentina, Buenos Aires, Argentina (F.C.); and Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (C.B., L.J.S.)
Tomato (Solanum lycopersicum) is a well-studied model of fleshy fruit development and ripening. Tomato fruit development is well understood from a hormonal-regulatory perspective, and developmental changes in pigment and cell wall metabolism are also well characterized. However, more general aspects of metabolic change during fruit development have not been studied despite the importance of metabolism in the context of final composition of the ripe fruit. In this study, we quantified the abundance of a broad range of metabolites by gas chromatography-mass spectrometry, analyzed a number of the principal metabolic fluxes, and in parallel analyzed transcriptomic changes during tomato fruit development. Metabolic profiling revealed pronounced shifts in the abundance of metabolites of both primary and secondary metabolism during development. The metabolite changes were reflected in the flux analysis that revealed a general decrease in metabolic activity during ripening. However, there were several distinct patterns of metabolite profile, and statistical analysis demonstrated that metabolites in the same (or closely related) pathways changed in abundance in a coordinated manner, indicating a tight regulation of metabolic activity. The metabolite data alone allowed investigations of likely routes through the metabolic network, and, as an example, we analyze the operational feasibility of different pathways of ascorbate synthesis. When combined with the transcriptomic data, several aspects of the regulation of metabolism during fruit ripening were revealed. First, it was apparent that transcript abundance was less strictly coordinated by functional group than metabolite abundance, suggesting that posttranslational mechanisms dominate metabolic regulation. Nevertheless, there were some correlations between specific transcripts and metabolites, and several novel associations were identified that could provide potential targets for manipulation of fruit compositional traits. Finally, there was a strong relationship between ripening-associated transcripts and specific metabolite groups, such as TCA-cycle organic acids and sugar phosphates, underlining the importance of the respective metabolic pathways during fruit development.
1 This work was supported by the Max Planck Society (in the form of a Max-Planck partner laboratory grant to F.C. and A.R.F.) and two independent grants in the BMBF GABI Program (to B.U. and to A.R.F. and M.-I.Z.), as well as by the Biotechnology and Biological Sciences Research Council (to C.B. and L.J.S.), CONICET, INTA, and EMBO (to F.C.).
The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instruction for Authors (www.plantphysiol.org) is: Alisdair R. Fernie (fernie{at}mpimp-golm.mpg.de).
[W] The online version of this article contains Web-only data.
www.plantphysiol.org/cgi/doi/10.1104/pp.106.088534
* Corresponding author; e-mail fernie{at}mpimp-golm.mpg.de; fax 49–331–5678408.
Received August 26, 2006;
accepted October 17, 2006;
published October 27, 2006.
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