pH-dependent transcriptional profile changes in iron-deficient Arabidopsis roots
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RESEARCH ARTICLE
Open Access
pH-dependent transcriptional profile changes in iron-deficient Arabidopsis roots Huei-Hsuan Tsai1 and Wolfgang Schmidt1,2,3*
Abstract Background: Iron is an essential element for plants and abundantly present in most mineral soils. The mobility of iron is, however, dependent on the redox potential and hydrogen activity (pH) of the soil, factors that may limit its availability to plants in particular at alkaline pHs. Iron deficiency triggers pronounced changes in the transcriptional profile of plants, inducing processes that aid in the acquisition, uptake, and translocation of iron. How ambient pH impact the transcriptional iron deficiency response has not yet been elucidated in detail. Results: Here, we provide an RNA-seq data set that catalogs global gene expression changes of iron-deficient plants grown at either optimal (5.5) or high (7.0) pH. A suite of 857 genes changed significantly and more than twofold in expression; only 54 genes of this suite were also differentially expressed between iron-deficient and ironsufficient plants grown at pH 5.5. Among the high pH-responsive genes, 186 were earlier shown to be responsive to short-term transfer to low pH, 91 genes of this subset were anti-directionally regulated by high and low pH. The latter subset contained genes involved in cell wall organization, auxin homeostasis, and potential hubs of yet undefined signaling circuits. Growing iron-deficient plants at high pH also modulated the transcriptional iron deficiency response observed at pH 5.5 by compromising the enzymatic reduction of ferric chelates and favoring the production of iron-mobilizing coumarins. Conclusions: It is concluded that ambient pH is an important determinant of global gene expression which tunes iron acquisition to the prevailing edaphic conditions. Keywords: Ambient pH, Coumarins, Iron deficiency, Iron uptake, RNA-seq, Transcriptome, Alkaline soil
Background Soil pH, i.e. the dynamic equilibrium of H+ activity between the soil solution and the negatively charged solid phase, is an important edaphic factor that dictates the availability of mineral nutrients, affects the composition of the microbiome, and determines the composition of plant communities through alterations in the availability of mineral nutrients in the soil [4]. Iron is highly abundant in most soils, but the low mobility of oxidized iron * Correspondence: [email protected] 1 Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan 2 Biotechnology Center, National Chung-Hsing University, Taichung 40227, Taiwan Full list of author information is available at the end of the article
compounds often limits its phyto-availability. In aerated soils, the solubility of iron decreases by a factor of 1000 for each unit increase in pH between 4 and 9, severely restricting the supply of iron at circumneutral or alkaline conditions [16]. In Arabidopsis and other non-grass species, iron starvation triggers a sophisticatedly regulated response comprising processes which increase
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