Abstract
BackgroundBeing sessile organisms, plants should adjust their metabolism to dynamic changes in their environment. Such adjustments need particular coordination in branched metabolic networks in which a given metabolite can be converted into multiple other metabolites via different enzymatic chains. In the present report, we developed a novel "Gene Coordination" bioinformatics approach and use it to elucidate adjustable transcriptional interactions of two branched amino acid metabolic networks in plants in response to environmental stresses, using publicly available microarray results.ResultsUsing our "Gene Coordination" approach, we have identified in Arabidopsis plants two oppositely regulated groups of "highly coordinated" genes within the branched Asp-family network of Arabidopsis plants, which metabolizes the amino acids Lys, Met, Thr, Ile and Gly, as well as a single group of "highly coordinated" genes within the branched aromatic amino acid metabolic network, which metabolizes the amino acids Trp, Phe and Tyr. These genes possess highly coordinated adjustable negative and positive expression responses to various stress cues, which apparently regulate adjustable metabolic shifts between competing branches of these networks. We also provide evidence implying that these highly coordinated genes are central to impose intra- and inter-network interactions between the Asp-family and aromatic amino acid metabolic networks as well as differential system interactions with other growth promoting and stress-associated genome-wide genes.ConclusionOur novel Gene Coordination elucidates that branched amino acid metabolic networks in plants are regulated by specific groups of highly coordinated genes that possess adjustable intra-network, inter-network and genome-wide transcriptional interactions. We also hypothesize that such transcriptional interactions enable regulatory metabolic adjustments needed for adaptation to the stresses.
Highlights
Being sessile organisms, plants should adjust their metabolism to dynamic changes in their environment
The Asp-family network includes the amino acids Lys, Thr and Met, Ile and Gly whose synthesis initiates from Asp, and in which one pathway leads to Lys metabolism (Fig. 1, enzymatic steps 1–8), a second pathway leads to Thr synthesis and its further conversion into Ile and Gly (Fig. 1, enzymatic steps, 2, 9, 10, 18–23), and the third pathway leads to Met metabolism (Fig. 1, enzymatic steps 2, 9–17)
The aromatic amino acids (AAA) network, whose synthesis initiates from chorismate, includes three pathways; one leading to Trp metabolism (Fig. 1, enzymatic steps 24–31), while the second and third pathways lead to Phe and Tyr metabolism
Summary
Plants should adjust their metabolism to dynamic changes in their environment. The adaptation mechanisms of plants to stresses involve coordinated adjustments of a large array of metabolic networks. Among those are metabolic networks containing amino acids as intermediate metabolites, which can either be incorporated into proteins, accumulate to high levels in response to specific cues, such as proline accumulation in (page number not for citation purposes). Two of the most important branched metabolic networks of amino acids are the Asp-family network and the aromatic amino acids (AAA) network (Fig. 1 panels A and B) These two networks possess significant nutritional value because humans and much of their farm animals cannot synthesize the amino acids produced by them and depend on plants as their nutritional supplements [2]
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