Abstract
In order to elucidate transcriptional and metabolic networks associated with lysine (Lys) metabolism, we utilized developing Arabidopsis (Arabidopsis thaliana) seeds as a system in which Lys synthesis could be stimulated developmentally without application of chemicals and coupled this to a T-DNA insertion knockout mutation impaired in Lys catabolism. This seed-specific metabolic perturbation stimulated Lys accumulation starting from the initiation of storage reserve accumulation. Our results revealed that the response of seed metabolism to the inducible alteration of Lys metabolism was relatively minor; however, that which was observable operated in a modular manner. They also demonstrated that Lys metabolism is strongly associated with the operation of the tricarboxylic acid cycle while largely disconnected from other metabolic networks. In contrast, the inducible alteration of Lys metabolism was strongly associated with gene networks, stimulating the expression of hundreds of genes controlling anabolic processes that are associated with plant performance and vigor while suppressing a small number of genes associated with plant stress interactions. The most pronounced effect of the developmentally inducible alteration of Lys metabolism was an induction of expression of a large set of genes encoding ribosomal proteins as well as genes encoding translation initiation and elongation factors, all of which are associated with protein synthesis. With respect to metabolic regulation, the inducible alteration of Lys metabolism was primarily associated with altered expression of genes belonging to networks of amino acids and sugar metabolism. The combined data are discussed within the context of network interactions both between and within metabolic and transcriptional control systems.
Highlights
Metabolism is one of the most important and best recognized networks within biological systems
In order to elucidate transcriptional and metabolic networks associated with Lys metabolism, we utilized developing seeds as a system in which Lys synthesis could be stimulated developmentally without application of chemicals and coupled this to a T-DNA insertion knockout mutation impaired in Lys catabolism
A Seed-Specific Developmentally Inducible System To Decipher Gene Expression And Metabolic Networks Associated With Lys Metabolism In order to elucidate novel network interactions of Lys metabolism with genome-wide gene expression programs and networks of primary metabolism, we utilized an Arabidopsis mutant (Zhu and Galili, 2003) displaying a seed-specific, developmentally-induced bacterial feedback-insensitive DHDPS enzyme of Lys biosynthesis in addition to a T-DNA knockout mutation in the LKR/SDH gene affected in Lys catabolism (Zhu and Galili, 2003)
Summary
Metabolism is one of the most important and best recognized networks within biological systems. To date, studies on metabolic regulation have mostly been limited to regulatory interactions within the metabolic pathways themselves. These studies have, amongst other things, revealed that amino acid biosynthesis generally occurs through branched pathways, which are considerably more complex than the non-branched pathway of glycolysis (Sweetlove and Fernie, 2005; Sweetlove et al, 2008). Lys metabolism was shown to be regulated both by the rate of its synthesis and catabolism via the α-amino adipic acid pathway (Zhu and Galili, 2004; Less and Galili, 2009). Notwithstanding the significant complexity of the pathway of Lys metabolism in plants, remarkably little is known concerning the influence of this pathway on genome-wide patterns of gene expression or of its impact on primary metabolism as a whole
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