Intron Retention in the 5′UTR of the Novel ZIF2 Transporter Enhances Translation to Promote Zinc Tolerance in Arabidopsis

Root vacuolar sequestration is one of the best-conserved plant strategies to cope with heavy metal toxicity. Here we report that zinc (Zn) tolerance in Arabidopsis requires the action of a novel Major Facilitator Superfamily (MFS) transporter. We show that ZIF2 (Zinc-Induced Facilitator 2) localises primarily at the tonoplast of root cortical cells and is a functional transporter able to mediate Zn efflux when heterologously expressed in yeast. By affecting plant tissue partitioning of the metal ion, loss of ZIF2 function exacerbates plant sensitivity to excess Zn, while its overexpression enhances Zn tolerance. The ZIF2 gene is Zn-induced and an intron retention event in its 5′UTR generates two splice variants ( ZIF2.1 and ZIF2.2 ) encoding the same protein. Importantly, high Zn favours production of the longer ZIF2.2 transcript, which compared to ZIF2.1 confers greater Zn tolerance to transgenic plants by promoting higher root Zn immobilization. We show that the retained intron in the ZIF2 5′UTR enhances translation in a Zn-responsive manner, markedly promoting ZIF2 protein expression under excess Zn. Moreover, Zn regulation of translation driven by the ZIF2.2 5′UTR depends largely on a predicted stable stem loop immediately upstream of the start codon that is lost in the ZIF2.1 5′UTR. Collectively, our findings indicate that alternative splicing controls the levels of a Zn-responsive mRNA variant of the ZIF2 transporter to enhance plant tolerance to the metal ion. Alternative splicing, which generates multiple messenger RNAs (mRNAs) from the same gene, is a key posttranscriptional regulatory mechanism in higher eukaryotes whose functional relevance in plants remains poorly understood. The sequestration of metal ions inside the vacuole of root cells is an important strategy employed by plants to cope with heavy metal toxicity. Here, we describe a new vacuolar membrane transporter of the model plant Arabidopsis thaliana , ZIF2, that confers tolerance to zinc (Zn) by promoting root immobilisation of the metal ion and thus its exclusion from the aerial parts of the plant. The ZIF2 gene is induced by exposure to excess Zn and undergoes alternative splicing, generating two mRNAs that differ solely in their non-coding regions and hence code for the same transporter. Interestingly, toxic Zn levels favour expression of the longer mRNA, which in turn confers higher plant tolerance to the metal. We show that the longer ZIF2 non-coding region markedly promotes tran