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

Hans-Jörg Mai,Stéphanie Pateyron,Petra Bauer

doi:10.1186/s12870-016-0899-9

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.

Highlights

FIT (FER-LIKE IRON DEFICIENCY-INDUCED TRANSCRIPTION FACTOR) is the central regulator of iron uptake in Arabidopsis thaliana roots
We first analyzed the transcriptomic changes in roots of six week-old wild type, fit and HA-FIT plants that were exposed to iron-sufficient (+Fe) or irondeficient (-Fe) conditions for 7 days prior to harvesting and the same analyses were conducted with six-day-old whole seedlings that were grown on +Fe or -Fe (Additional file 1: Figure S1)
We suggest as a possible explanation that along with the robustly FIT-dependent genes other distinct sets of genes could be under the control of additional but yet unknown factors which might act in different developmental stages

Summary

Introduction

FIT (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 ironsufficient 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. Mai et al BMC Plant Biology (2016) 16:211 only under iron deficient conditions [11] and ectopic expression of IRT1 and FRO2 in leaves only occurs under iron deficiency [12]. Loss-of-function mutants of fit exhibit symptoms of iron starvation like chlorosis, reduced growth and lethality [11, 12, 18]

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