Coordinations between gene modules control the operation of plant amino acid metabolic networks.
BACKGROUND
Being 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.


RESULTS
Using 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.


CONCLUSIONS
Our 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.
Less
Hadar
H
Department of Plant Sciences, the Weizmann Institute of Science, Rehovot 76100, Israel. hadar.less@weizmann.ac.il
Galili
Gad
G
D000596:Amino Acids / Q000378:metabolism*; D024322:Amino Acids, Aromatic / Q000378:metabolism; D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism*; D001224:Aspartic Acid / Q000378:metabolism; D019295:Computational Biology; D053263:Gene Regulatory Networks; D018745:Genome, Plant; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis / Q000706:statistics & numerical data; D013312:Stress, Physiological; D049490:Systems Biology
D000596:Amino Acids; D024322:Amino Acids, Aromatic; D001224:Aspartic Acid