Integrated Analysis of Metabolite and Transcript Levels Reveals the Metabolic Shifts That Underlie Tomato Fruit Development and Highlight Regulatory Aspects of Metabolic Network Behavior

Abstract

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.

Comprehensive Tissue-Specific Transcriptome Analysis Reveals Distinct Regulatory Programs during Early Tomato Fruit Development

“…4). This suggests an early metabolic specialization of the pericarp for the production of isoprenoid-derived metabolites, such as carotenoids, neoxanthin, and the phytol tail of chlorophylls, all of which accumulate in young fruit (Carrari et al, 2006). Our results also indicate that photosynthesis-related genes are tightly coexpressed and show strong tissue dependency, being expressed at higher levels in internal tissues.…”

An Orange Ripening Mutant Links Plastid NAD(P)H Dehydrogenase Complex Activity to Central and Specialized Metabolism during Tomato Fruit Maturation

“…Intriguingly, significant decrease was observed in the levels of Ala, Lys, and Pro (in both Orr Ds /ORR and Orr Ds /Orr Ds ); in Asp, Trp, succinate, and glucose (in Orr Ds /ORR); and in glutamate and maltose (in Orr Ds /Orr Ds ). Given that these metabolites normally increase during ripening (Roessner-Tunali et al, 2003;Carrari et al, 2006), this result suggests an alteration in the nature of ripening of the Orr Ds fruit.…”

Clustering biological data with SOMs: On topology preservation in non-linear dimensional reduction

“…The biological dataset used in this study has 2458 values obtained from transcriptional profiles and metabolic accumulation of S. lycopersicum x S. pennellii introgression lines (ILs) [26]. The ILs harbor, in certain chromosome segments, introgressed portions of the wild Solanum species (Solanum pennelli ).…”