title: Identification of candidate network hubs involved in metabolic adjustments of rice under drought stress by integrating transcriptome data and genome-scale metabolic network.
abstract: In this study, we have integrated a rice genome-scale metabolic network and the transcriptome of a drought-tolerant rice line, DK151, to identify the major transcriptional regulators involved in metabolic adjustments necessary for adaptation to drought. This was achieved by examining the differential expressions of transcription factors and metabolic genes in leaf, root and young panicle of rice plants subjected to drought stress during tillering, booting and panicle elongation stages. Critical transcription factors such as AP2/ERF, bZIP, MYB and NAC that control the important nodes in the gene regulatory pathway were identified through correlative analysis of the patterns of spatio-temporal expression and cis-element enrichment. We showed that many of the candidate transcription factors involved in metabolic adjustments were previously linked to phenotypic variation for drought tolerance. This approach represents the first attempt to integrate models of transcriptional regulation and metabolic pathways for the identification of candidate regulatory genes for targeted selection in rice breeding.
authors.affiliation: Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, 117585 Singapore.
authors.forename: Bijayalaxmi
authors.initials: B
authors.lastname: Mohanty
authors.affiliation: School of Biology and Ecology, University of Maine, Orono, ME 04469 USA.
authors.forename: Ai
authors.initials: A
authors.lastname: Kitazumi
authors.affiliation: Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, 117585 Singapore.
authors.forename: C Y Maurice
authors.initials: CYM
authors.lastname: Cheung
authors.affiliation: Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Centros, 138668 Singapore.
authors.forename: Meiyappan
authors.initials: M
authors.lastname: Lakshmanan
authors.affiliation: School of Biology and Ecology, University of Maine, Orono, ME 04469 USA.
authors.forename: Benildo G
authors.initials: BG
authors.lastname: de Los Reyes
authors.affiliation: Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, 117604 Singapore; Department of Biological Sciences, National University of Singapore,14 Science Drive 4, 117543 Singapore.
authors.forename: In-Cheol
authors.initials: IC
authors.lastname: Jang
authors.affiliation: Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, 117585 Singapore; Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Centros, 138668 Singapore. Electronic address: cheld@nus.edu.sg.
authors.forename: Dong-Yup
authors.initials: DY
authors.lastname: Lee
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D001483:Base Sequence; D016000:Cluster Analysis; D055864:Droughts; D020869:Gene Expression Profiling / Q000379:methods*; D053263:Gene Regulatory Networks; D018745:Genome, Plant / Q000235:genetics*; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D008957:Models, Genetic; D059372:Nucleotide Motifs / Q000235:genetics; D012275:Oryza / Q000235:genetics*; D000069600:Plant Breeding / Q000379:methods; D010940:Plant Proteins / Q000145:classification / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics; D013312:Stress, Physiological / Q000235:genetics; D014157:Transcription Factors / Q000145:classification / Q000235:genetics
chemical_list: D010940:Plant Proteins; D014157:Transcription Factors
keywords: Drought; Metabolic network; Physiological adjustment; Plant breeding; Transcription factor; cis-elements