Characterization of Transcriptiomic and Metabolic Networks, Regulating Arabidopsis Seed Maturation and Germination

Whilst the metabolic networks in developing seeds during the period of reserve accumulation have been extensively characterized, much less is known about those present during seed desiccation and subsequent germination. In this study we utilized metabolite and transcripts profiling, in conjunction with physiological profiling approach to characterize Arabidopsis seeds ( Arabidopsis thaliana) throughout development and germination. Seed maturation was associated with a significant reduction of most sugars, organic acids and amino acids, suggesting their efficient incorporation into storage reserves. The transition from reserve accumulation to seed desiccation was associated with a major metabolic switch, resulting in the accumulation of distinct sugars, organic acids, nitrogen-rich amino acids and shikimate-derived metabolites. In contrast, early germination seed (vernalization/stratification) was associated with a decrease in the content of several of the metabolic intermediates accumulated during seed desiccation, implying that these intermediates might support the metabolic reorganization needed for seed germination. Concomitantly, the levels of other metabolites significantly increased during vernalization and were boosted further during germination sensu stricto, implying their importance for germination and seedling establishment. The metabolic switches during seed maturation and germination were also associated with distinct patterns of expression of genes encoding metabolism-associated gene products, as determined by semi-quantitative RT-PCR and analysis of publicly available microarray data.;To further elucidate novel regulatory principles of seed maturation and germination, we subjected maturating and germinating seeds of an Arabidopsis mutant possessing a seed-specific alteration of Lys metabolism to transcript, metabolite and proteomic analyses. Lys over-accumulation was most pronounced during late seed maturation, implying a major activity of amino acid metabolism in desiccating seeds. In addition, our results showed that seed metabolism and also its response to the altered Lys metabolism operate in a modular manner; and that Lys metabolism is strongly associated with the operation of the TCA cycle whilst largely disconnected from other metabolic networks in maturing seeds. In addition, we also observed that whilst currently defined master regulatory genes of seed maturation do not respond to the altered Lys metabolism, a number of other genes, which apparently operate downstream to them, are clearly metabolically regulated. These genes encode various regulatory proteins, such as translation factors, chromatin remodeling proteins and transcription factors, including a novel transcription factor of heat shock genes that are known to be involved in the tolerance of seed to desiccation. Furthermore, the mutant with altered Lys metabolism displays defective desiccation as evidenced by the altered solubility of its storage proteins. As a consequence radicle protrusion is severely inhibited during early germination despite the fact that only a minor subset of the regulatory genes, and recently defined metabolic components associated with germination, are altered. When taken together our results provide a comprehensive picture of the co-ordinated changes in primary metabolism that underlie seed development and germination in Arabidopsis. They furthermore, imply that the metabolic preparation for germination and efficient seedling establishment initiates already during seed desiccation and continues by additional distinct metabolic switches during vernalization and early germination. In addition the combined data are discussed within the context of current models defining the regulatory processes which integrate maturation and germination of seeds.