title: Co-expression analysis reveals a group of genes potentially involved in regulation of plant response to iron-deficiency.
abstract: Iron (Fe) is an essential element for plant growth and development. Iron deficiency results in abnormal metabolisms from respiration to photosynthesis. Exploration of Fe-deficient responsive genes and their networks is critically important to understand molecular mechanisms leading to the plant adaptation to soil Fe-limitation. Co-expression genes are a cluster of genes that have a similar expression pattern to execute relatively biological functions at a stage of development or under a certain environmental condition. They may share a common regulatory mechanism. In this study, we investigated Fe-starved-related co-expression genes from Arabidopsis. From the biological process GO annotation of TAIR (The Arabidopsis Information Resource), 180 iron-deficient responsive genes were detected. Using ATTED-II database, we generated six gene co-expression networks. Among these, two modules of PYE and IRT1 were successfully constructed. There are 30 co-expression genes that are incorporated in the two modules (12 in PYE-module and 18 in IRT1-module). Sixteen of the co-expression genes were well characterized. The remaining genes (14) are poorly or not functionally identified with iron stress. Validation of the 14 genes using real-time PCR showed differential expression under iron-deficiency. Most of the co-expression genes (23/30) could be validated in pye and fit mutant plants with iron-deficiency. We further identified iron-responsive cis-elements upstream of the co-expression genes and found that 22 out of 30 genes contain the iron-responsive motif IDE1. Furthermore, some auxin and ethylene-responsive elements were detected in the promoters of the co-expression genes. These results suggest that some of the genes can be also involved in iron stress response through the phytohormone-responsive pathways.
authors.affiliation: Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China; Department of Plant Science, College of Life Science, Henan Agricultural University, Henan 450002, China.
authors.forename: Hua
authors.initials: H
authors.lastname: Li
authors.affiliation: Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China.
authors.forename: Lei
authors.initials: L
authors.lastname: Wang
authors.affiliation: Department of Biochemistry and Molecular Biology, College of Life Science, Nanjing Agricultural University, Nanjing 210095, China. Electronic address: zmyang@njau.edu.cn.
authors.forename: Zhi Min
authors.initials: ZM
authors.lastname: Yang
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics; D051792:Basic Helix-Loop-Helix Proteins / Q000235:genetics; D027682:Cation Transport Proteins / Q000235:genetics; D019295:Computational Biology; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D000090463:Iron Deficiencies; D005810:Multigene Family; D009154:Mutation; D018517:Plant Roots / Q000235:genetics; D011401:Promoter Regions, Genetic
chemical_list: D029681:Arabidopsis Proteins; D051792:Basic Helix-Loop-Helix Proteins; D027682:Cation Transport Proteins; C099651:IRT1 protein, Arabidopsis
keywords: Arabidopsis thaliana; Co-expression analysis; IRT1; Iron deficiency; PYE