A Combined Proteome and Transcriptome Analysis of Developing Medicago truncatula Seeds EVIDENCE FOR METABOLIC SPECIALIZATION OF MATERNAL AND FILIAL TISSUES*□S

A comparative study of proteome and transcriptome changes during Medicago truncatula (cultivar Jemalong) seed development has been carried out. Transcript and protein profiles were parallel across the time course for 50% of the comparisons made, but divergent patterns were also observed, indicative of post-transcriptional events. These data, combined with the analysis of transcript and protein distribution in the isolated seed coat, endosperm, and embryo, demonstrated the major contribution made to the embryo by the surrounding tissues. First, a remarkable compartmentalization of enzymes involved in methionine biosynthesis between the seed tissues was revealed that may regulate the availability of sulfur-containing amino acids for embryo protein synthesis during seed filling. This intertissue compartmentalization, which was also apparent for enzymes of sulfur assimilation, is relevant to strategies for modifying the nutritional value of legume seeds. Second, decreasing levels during seed filling of seed coat and endosperm metabolic enzymes, including essential steps in Met metabolism, are indicative of a metabolic shift from a highly active to a quiescent state as the embryo assimilates nutrients. Third, a concomitant persistence of several proteases in seed coat and endosperm highlighted the importance of proteolysis in these tissues as a supplementary source of amino acids for protein synthesis in the embryo. Finally, the data revealed the sites of expression within the seed of a large number of transporters implied in nutrient import and intraseed translocations. Several of these, including a sulfate transporter, were preferentially expressed in seeds compared with other plant organs. These findings provide new directions for genetic improvement of grain legumes. Molecular & Cellular Proteomics 6:2165–2179, 2007. Seed development starts with the formation of a protective seed coat, the testa, derived from the maternal ovule integuments, which enclose the filial compartments, the endosperm, and embryo. These tissues are in dynamic interaction, as shown by the recent report that the maternal control of seed coat cell elongation and the zygotic control of endosperm growth are coordinated to determine seed size in Arabidopsis (Arabidopsis thaliana) (1). Once these tissues are differentiated, storage compounds accumulate in the endosperm and/or embryo, depending on the species, desiccation tolerance is acquired, and finally metabolic activity declines to a quiescent state (2, 3). At maturity, seed coats were found to be the primary determinant of seed dormancy (4). During seed filling, the young seed coat supports storage compound synthesis in the filial tissues by transmitting organic nutrients from the phloem, mainly sugars, glutamine, and asparagine (5). Phloem sulfur supply in the form of sulfate, S-methylmethionine (SMM) and glutathione, also influences significantly seed composition (6, 7). The morphology and composition of the filial organs vary greatly among species. In mature seeds of the Gramineae, the endosperm serves as the major filial storage tissue, rich in starch but with a protein content of less than 16%. In contrast, the principal storage organ of grain legumes is the cotyledon with protein contents ranging from 20% to as much as 40%, and the mature seed has little endosperm tissue. Like the major storage proteins of barley and maize grains (prolamin, glutelin), the predominant proteins of legume seeds (legumin, vicilin) are low in tryptophan ( 1%) and in the sulfur-containing amino acids cysteine and methionine ( 1.5%). The nature of the storage proteins that determine the amino acid composition of the total protein