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Lin, WD, Liao, YY, Yang, TJ, Pan, CY, Buckhout, TJ and Schmidt, W (2011) Coexpression-based clustering of Arabidopsis root genes predicts functional modules in early phosphate deficiency signaling. Plant Physiol. 155:1383-402

Phosphate (Pi) deficiency triggers the differential expression of a large set of genes, which communally adapt the plant to low Pi bioavailability. To infer functional modules in early transcriptional responses to Pi deficiency, we conducted time-course microarray experiments and subsequent coexpression-based clustering of Pi-responsive genes by pairwise comparison of genes against a customized database. Three major clusters, enriched in genes putatively functioning in transcriptional regulation, root hair formation, and developmental adaptations, were predicted from this analysis. Validation of gene expression by quantitative reverse transcription-PCR revealed that transcripts from randomly selected genes were robustly induced within the first hour after transfer to Pi-deplete medium. Pectin-related processes were among the earliest and most robust responses to Pi deficiency, indicating that cell wall alterations are critical in the early transcriptional response to Pi deficiency. Phenotypical analysis of homozygous mutants defective in the expression of genes from the root hair cluster revealed eight novel genes involved in Pi deficiency-induced root hair elongation. The plants responded rapidly to Pi deficiency by the induction of a subset of transcription factors, followed by a repression of genes involved in cell wall alterations. The combined results provide a novel, integrated view at a systems level of the root responses that acclimate Arabidopsis (Arabidopsis thaliana) to suboptimal Pi levels.

PubMed PMC3046593 Online version:10.1104/pp.110.166520

Arabidopsis/drug effects; Arabidopsis/genetics; Arabidopsis/growth & development; DNA, Bacterial/genetics; Gene Expression Regulation, Plant/drug effects; Gene Regulatory Networks/genetics; Genes, Plant/genetics; Homozygote; Multigene Family/genetics; Mutagenesis, Insertional/drug effects; Mutagenesis, Insertional/genetics; Mutation/genetics; Organ Specificity/drug effects; Organ Specificity/genetics; Phenotype; Phosphates/deficiency; Phosphates/pharmacology; Plant Roots/drug effects; Plant Roots/genetics; Plant Roots/growth & development; Signal Transduction/drug effects; Signal Transduction/genetics; Software; Time Factors