Spatial transcriptomes of iron-deficient and cadmium-stressed rice.
New Phytol, 2014/2;201(3):781-794.
Ogo Y[1], Kakei Y[1], Itai RN[1], Kobayashi T[1, 2], Nakanishi H[1], Takahashi H[3], Nakazono M[3], Nishizawa NK[1, 2]
Affiliations
PMID: 24188410DOI: 10.1111/nph.12577
Impact factor: 10.323
Abstract
Although the genes involved in metal homeostasis have been investigated over the past few decades, many genes related to metal homeostasis remain uncharacterized, and a comprehensive analysis of the expression of these genes is required. In the present study, we investigated the spatial gene expression profile of iron (Fe)-deficient and cadmium (Cd)-stressed Oryza sativa (rice) using laser microdissection and microarray analysis. Roots of Fe-deficient and Cd-stressed rice were separated into the vascular bundle, cortex, and epidermis plus exodermis. In addition, vascular bundles from new and old leaves at the lowest node, which are important for metal distribution, were analyzed separately. The spatial expression patterns were distinct in each tissue type. Fe deficiency and Cd stress also had significant effects on the transcriptomes, although these were less pronounced than the spatial effects. Genes encoding transporters involved in metal homeostasis, proteins associated with heavy metal detoxification, and phytohormone-related proteins were comprehensively investigated. Additionally, cis motifs involved in the regulation of these diverse expression changes in various tissue types were predicted. The spatial transcriptomes presented here provide novel insight into the molecular mechanisms of metal homeostasis.
Keywords: Oryza sativa (rice); cadmium (Cd); iron (Fe); laser microdissection; transcriptome
MeSH terms
Base Sequence; Biological Transport; Cadmium; Cluster Analysis; Gene Expression Profiling; Gene Expression Regulation, Plant; Gene Regulatory Networks; Genes, Plant; Homeostasis; Iron Deficiencies; Laser Capture Microdissection; Molecular Sequence Data; Nucleotide Motifs; Oligonucleotide Array Sequence Analysis; Organ Specificity; Oryza; Plant Growth Regulators; Plant Proteins; Plant Roots; Promoter Regions, Genetic; Siderophores; Signal Transduction; Stress, Physiological; Transcriptome; Up-Regulation
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