A Digital Compendium of Genes Mediating the Reversible Phosphorylation of Proteins in Fe-Deficient Arabidopsis Roots

Abstract

Post-translational modifications of proteins such as reversible phosphorylation provide an important but understudied regulatory network that controls important nodes in the adaptation of plants to environmental conditions. Iron (Fe) is an essential mineral nutrient for plants, but due to its low solubility often a limiting factor for optimal growth. To understand the role of protein phosphorylation in the regulation of cellular Fe homeostasis, we analyzed the expression of protein kinases (PKs) and phosphatases (PPs) in Arabidopsis roots by mining differentially expressed PK and PP genes. Transcriptome analysis using RNA-seq revealed that subsets of 203 PK and 39 PP genes were differentially expressed under Fe-deficient conditions. Functional modules of these PK and PP genes were further generated based on co-expression analysis using the MACCU toolbox on the basis of 300 publicly available root-related microarray data sets. Results revealed networks comprising 87 known or annotated PK and PP genes that could be subdivided into one large and several smaller highly co-expressed gene modules. The largest module was composed of 58 genes, most of which have been assigned to the leucine-rich repeat protein kinase superfamily and associated with the biological processes “hypotonic salinity response,” “potassium ion import,” and “cellular potassium ion homeostasis.” The comprehensive transcriptional information on PK and PP genes in iron-deficient roots provided here sets the stage for follow-up experiments and contributes to our understanding of the post-translational regulation of Fe deficiency and potassium ion homeostasis.

The Understanding of the Plant Iron Deficiency Responses in Strategy I Plants and the Role of Ethylene in This Process by Omic Approaches

“…Is it possible to transport Met under Fe deficiency? Indeed, as mentioned above, the gene encoding MTK was robustly up-regulated by Fe deficiency (Dinneny et al, 2008; Garcia et al, 2010; Yang et al, 2010; Lan et al, 2013b; Mai et al, 2016). MTK is a key kinase of Yang-cycle involved in the Met salvage by phosphorylating methylthioribose (MTR).…”

“…Since 2001, toward the genome-wide understanding of plant response to Fe deficiency, transcriptome profiling studies, using custom-made or commercial-based microarrays and next-generation sequencing-based techniques (RNA-seq), have been carried out in a broad range of plant species, including model strategy I plant Arabidopsis, Medicago, soybean, as well as Strategy II plant rice and others (Thimm et al, 2001; Wang et al, 2003; Colangelo and Guerinot, 2004; Besson-Bard et al, 2009; Buckhout et al, 2009; Garcia et al, 2010; Sivitz et al, 2012; Zamboni et al, 2012; Li et al, 2013; Lan et al, 2013b; Rodriguez-Celma et al, 2013b; Bashir et al, 2014; Pan et al, 2015; Mai et al, 2016). Most of these omic studies have been carried out in the wild type plants either in Fe-deficient roots or shoots, also in the whole seedlings, while few of them are performed either in the ethylene mutants under Fe deficiency (Bauer and Blondet, 2011) or under Fe deficiency with ethylene inhibitors (Garcia et al, 2010).…”

“…Since most of extensive transcriptomic studies focused on the model plant Arabidopsis, the core Fe-responsive genes are depicted here for Arabidopsis. Three microarray studies relying on commercially available Affymetrix ATH1 GeneChips (Dinneny et al, 2008; Yang et al, 2010; Mai et al, 2016) and one RNA-seq data set (Lan et al, 2013b) have been chosen for this attempt. The reason for choosing these studies is below: (1) the plants used in all these studies were similar age; (2) all these studies provided both up- and down-regulated genes upon Fe deficiency; (3) all these studies provided differentially expressed genes in wild type plants.…”

Proteomics in Deciphering the Auxin Commitment in the Arabidopsis thaliana Root Growth

“…14,15 More recently, RNA-seq technology is providing genome-scale transcriptional maps of the genes involved in the responsiveness of the A. thaliana root to environmental stimuli. [16][17][18][19] Moreover, well-characterized transgenic lines expressing green fluorescent protein (GFP) in specific cell populations have been made available. These lines allow cell-type specific molecular profiling via Fluorescent Activated Cell Sorting (FACS) methodology.…”

Cellular Iron homeostasis and metabolism in plant

“…In particular, Lan et al (2013) investigated the role of protein phosphorylation in the regulation of cellular Fe homeostasis, by using RNA-seq analysis. The authors revealed networks comprising 87 known or annotated protein kinase and phosphatase genes that could be subdivided into several co-expressed gene modules, assigned to the leucine-rich repeat protein kinase superfamily or associated with biological processes such as "hypotonic salinity response," "potassium ion import," and "cellular potassium ion homeostasis."…”