Iron homeostasis in Arabidopsis thaliana: transcriptomic analyses reveal novel FIT-regulated genes, iron deficiency marker genes and functional gene networks

Abstract

BackgroundFIT (FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR) is the central regulator of iron uptake in Arabidopsis thaliana roots. We performed transcriptome analyses of six day-old seedlings and roots of six week-old plants using wild type, a fit knock-out mutant and a FIT over-expression line grown under iron-sufficient or iron-deficient conditions. We compared genes regulated in a FIT-dependent manner depending on the developmental stage of the plants. We assembled a high likelihood dataset which we used to perform co-expression and functional analysis of the most stably iron deficiency-induced genes.Results448 genes were found FIT-regulated. Out of these, 34 genes were robustly FIT-regulated in root and seedling samples and included 13 novel FIT-dependent genes. Three hundred thirty-one genes showed differential regulation in response to the presence and absence of FIT only in the root samples, while this was the case for 83 genes in the seedling samples. We assembled a virtual dataset of iron-regulated genes based on a total of 14 transcriptomic analyses of iron-deficient and iron-sufficient wild-type plants to pinpoint the best marker genes for iron deficiency and analyzed this dataset in depth. Co-expression analysis of this dataset revealed 13 distinct regulons part of which predominantly contained functionally related genes.ConclusionsWe could enlarge the list of FIT-dependent genes and discriminate between genes that are robustly FIT-regulated in roots and seedlings or only in one of those. FIT-regulated genes were mostly induced, few of them were repressed by FIT. With the analysis of a virtual dataset we could filter out and pinpoint new candidates among the most reliable marker genes for iron deficiency. Moreover, co-expression and functional analysis of this virtual dataset revealed iron deficiency-induced and functionally distinct regulons.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0899-9) contains supplementary material, which is available to authorized users.

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.…”

Iron-Nicotianamine Transporters Are Required for Proper Long Distance Iron Signaling

“…Notably, even though the proportion of genes with appropriate expression is higher in leaves, a large fraction (32.8%) of the iron-regulated genes in leaves of DM plants had Table I. Comparison of the expression of select iron deficiency-regulated genes (Petit et al, 2001;Stacey et al, 2002Stacey et al, , 2008Mukherjee et al, 2006;Schaaf et al, 2006;Wang et al, 2007;Klatte et al, 2009;Haydon et al, 2012;Palmer et al, 2013;Fourcroy et al, 2016;Mai et al, 2016;Sisó -Terraza et al, 2016;Yan et al, 2016;Ziegler et al, 2017) (Petit et al, 2001;Stacey et al, 2002Stacey et al, , 2008Mukherjee et al, 2006;Cohu and Pilon, 2007;Wang et al, 2007;Klatte et al, 2009) in ysl1ysl3 DM and wild-type shoots *, P , 0.05; **, P , 0.001; N.S. indicates that the difference was not significant (P .…”

“…In Arabidopsis, the genes most directly responsible for iron uptake are the Fe(II) transporter IRT1 (Eide et al, 1996;Henriques et al, 2002;Varotto et al, 2002;Vert et al, 2002) and the ferric chelate reductase FRO2 (Robinson et al, 1999;Connolly et al, 2003). Both these genes are strongly up-regulated by iron deficiency, and regulatory proteins governing the expression of these genes have been the subject of intense investigation (Colangelo and Guerinot, 2004;Jakoby et al, 2004;Yuan et al, 2005Yuan et al, , 2008Bauer et al, 2007;Wang et al, 2007;Long et al, 2010;Selote et al, 2015;Li et al, 2016;Mai et al, 2016). An additional component of iron uptake in nongraminaceous plants is the discovery that iron deficiency induces the secretion of phenolics and flavins (Rodríguez-Celma et al, 2013), later better defined as coumarins (Schmid et al, 2014) that are secreted by the ABCG37/PDR9 transporter (Fourcroy et al, 2014).…”