In addition to light and water, CO(2) and mineral elements are required for plant growth and development. Among these factors, nitrogen is critical, since it is needed to synthesize amino acids, which are the building elements of protein, nucleotides, chlorophyll, and numerous other metabolites and cellular components. Therefore, nitrogen is required by plants in higher quantities and this investment in nitrogen supports the use of CO(2), water, and inorganic nitrogen to produce sugars, organic acids, and amino acids, the basic building blocks of biomass accumulation. This system is maintained by complex metabolic machinery, which is regulated at different levels according to environmental factors such as light, CO(2), and nutrient availability. Plants integrate these signals via a signaling network, which involves metabolites as well as nutrient-sensing proteins. Due to its importance, much research effort has been expended to understand how carbon and nitrogen metabolism are integrated and regulated according to the rates of photosynthesis, photorespiration, and respiration. Thus, in this article, we both discuss recent advances in carbon/nitrogen metabolisms as well as sensing and signaling systems in illuminated leaves of C3-plants and provide a perspective of the type of experiments that are now required in order to take our understanding to a higher level.

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.