title: Deciphering energy-associated gene networks operating in the response of Arabidopsis plants to stress and nutritional cues.
abstract: Plants need to continuously adjust their transcriptome in response to various stresses that lead to inhibition of photosynthesis and the deprivation of cellular energy. This adjustment is triggered in part by a coordinated re-programming of the energy-associated transcriptome to slow down photosynthesis and activate other energy-promoting gene networks. Therefore, understanding the stress-related transcriptional networks of genes belonging to energy-associated pathways is of major importance for engineering stress tolerance. In a bioinformatics approach developed by our group, termed 'gene coordination', we previously divided genes encoding for enzymes and transcription factors in Arabidopsis thaliana into three clusters, displaying altered coordinated transcriptional behaviors in response to multiple biotic and abiotic stresses (Plant Cell, 23, 2011, 1264). Enrichment analysis indicated further that genes controlling energy-associated metabolism operate as a compound network in response to stress. In the present paper, we describe in detail the network association of genes belonging to six central energy-associated pathways in each of these three clusters described in our previous paper. Our results expose extensive stress-associated intra- and inter-pathway interactions between genes from these pathways, indicating that genes encoding proteins involved in energy-associated metabolism are expressed in a highly coordinated manner. We also provide examples showing that this approach can be further utilized to elucidate candidate genes for stress tolerance and functions of isozymes.
authors.affiliation: Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel.
authors.forename: Tamar
authors.initials: T
authors.lastname: Avin-Wittenberg
authors.forename: Vered
authors.initials: V
authors.lastname: Tzin
authors.forename: Ruthie
authors.initials: R
authors.lastname: Angelovici
authors.forename: Hadar
authors.initials: H
authors.lastname: Less
authors.forename: Gad
authors.initials: G
authors.lastname: Galili
mesh_terms: D000251:Adenosine Triphosphatases / Q000096:biosynthesis; D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D002952:Citric Acid Cycle; D019295:Computational Biology; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D006019:Glycolysis; D010788:Photosynthesis; D013312:Stress, Physiological; D045725:Tetrapyrroles / Q000096:biosynthesis; D014158:Transcription, Genetic; D059467:Transcriptome
chemical_list: D045725:Tetrapyrroles; D000251:Adenosine Triphosphatases