[en] In Arabidopsis thaliana, FRD3 (Ferric Chelate Reductase Defective 3) plays a central role in metal homeostasis. FRD3 is among a set of metal homeostasis genes that are constitutively highly expressed in roots and shoots of Arabidopsis halleri, a zinc hyperaccumulating and hypertolerant species. Here, we examined the regulation of FRD3 by zinc in both species to shed light on the evolutionary processes underlying the evolution of hyperaccumulation in A. halleri. We combined gene expression studies with the use of GUS and GFP reporter constructs to compare the expression profile, transcriptional and post-transcriptional regulation of FRD3 in both species. The AtFRD3 and AhFRD3 genes display a conserved expression profile. In A. thaliana, alternative transcription initiation sites from two promoters determine transcript variants which are differentially regulated by zinc supply in roots and shoots to favour the most highly translated variant under zinc excess conditions. In A. halleri, a single transcript variant with higher transcript stability and enhanced translation has been maintained. The FRD3 gene thus undergoes complex transcriptional and post-transcriptional regulation in Arabidopsis relatives. Our study reveals that a diverse set of mechanisms underlie increased gene dosage in the A. halleri lineage and illustrates how an environmental challenge can alter gene regulation.
Alatorre-Cobos F, Cruz-Ramírez A, Hayden CA, Pérez-Torres C-A, Chauvin A-L, Ibarra-Laclette E, Alva-Cortés E, Jorgensen RA, Herrera-Estrella L. 2012. Translational regulation of Arabidopsis XIPOTL1 is modulated by phosphocholine levels via the phylogenetically conserved upstream open reading frame 30. Journal of Experimental Botany 63, 5203-5221.
Alvarez-Fernández A, Díaz-Benito P, Abadía A, López-Millán AF, Abadía J. 2014. Metal species involved in long distance metal transport in plants. Frontiers in Plant Science 5, 105.
Baek D, Jiang J, Chung J-S, Wang B, Chen J, Xin Z, Shi H. 2011. Regulated AtHKT1 gene expression by a distal enhancer element and DNA methylation in the promoter plays an important role in salt tolerance. Plant and Cell Physiology 52, 149-161.
Benderoth M, Textor S, Windsor AJ, Mitchell-Olds T, Gershenzon J, Kroymann J. 2006. Positive selection driving diversification in plant secondary metabolism. Proceedings of the National Academy of Sciences, USA 103, 9118-9123.
Broadley MR, White PJ, Hammond JP, Zelko I, Lux A. 2007. Zinc in plants. New Phytologist 173, 677-702.
Brody JR, Calhoun ES, Gallmeier E, Creavalle TD, Kern SE. 2004. Ultra-fast high-resolution agarose electrophoresis of DNA and RNA using low-molarity conductive media. Biotechniques 37, 598, 600, 602.
Bugaut A, Balasubramanian S. 2012. 5′-UTR RNA G-quadruplexes: translation regulation and targeting. Nucleic Acids Research 40, 4727-4741.
Cao S, Kumimoto RW, Gnesutta N, Calogero AM, Mantovani R, Holt BF. 2014. A Distal CCAAT/NUCLEAR FACTOR Y complex promotes chromatin looping at the FLOWERING LOCUS T promoter and regulates the timing of flowering in Arabidopsis. The Plant Cell 26, 1009-1017.
Clauss MJ, Koch MA. 2006. Poorly known relatives of Arabidopsis thaliana. Trends in Plant Science 11, 449-459.
Cornu J, Deinlein U, Horeth S, Braun M, Schmidt H, Weber M, Persson DP, Husted S, Schjoerring JK, Clemens S. 2015. Contrasting effects of nicotianamine synthase knockdown on zinc and nickel tolerance and accumulation in the zinc/cadmium hyperaccumulator Arabidopsis halleri. New Phytologist 206, 738-750.
Courbot M, Willems G, Motte P, Arvidsson S, Roosens N, Saumitou-Laprade P, Verbruggen N. 2007. A major QTL for Cd tolerance in Arabidopsis halleri co-localizes with HMA4, a gene encoding a heavy metal ATPase. Plant Physiology 144, 1052-1065.
Curtis MD, Grossniklaus U. 2003. A gateway cloning vector set for high-throughput functional analysis of genes in planta. Plant Physiology 133, 462-469.
Davuluri R, Suzuki Y, Sugano S, Plass C, Huang T. 2008. The functional consequences of alternative promoter use in mammalian genomes. Trends in Genetics 24, 167-177.
Deinlein U, Weber M, Schmidt H, et al.. 2012. Elevated nicotianamine levels in Arabidopsis halleri roots play a key role in zinc hyperaccumulation. The Plant Cell 24, 708-723.
Delhaize E. 1996. A metal-accumulator mutant of Arabidopsis thaliana. Plant Physiology 111, 849-855.
Docquier S, Tillemans V, Deltour R, Motte P. 2004. Nuclear bodies and compartmentalization of pre-mRNA splicing factors in higher plants. Chromosoma 112, 255-266.
Dräger DB, Desbrosses-Fonrouge AG, Krach C, Chardonnens AN, Meyer RC, Saumitou-Laprade P, Krämer U. 2004. Two genes encoding Arabidopsis halleri MTP1 metal transport proteins co-segregate with zinc tolerance and account for high MTP1 transcript levels. The Plant Journal 39, 425-439.
Durrett TP, Gassmann W, Rogers EE. 2007. The FRD3-mediated efflux of citrate into the root vasculature is necessary for efficient iron translocation. Plant Physiology 144, 197-205.
Dvir S, Velten L, Sharon E, Zeevi D, Carey LB, Weinberger A, Segal E. 2013. Deciphering the rules by which 5?-UTR sequences affect protein expression in yeast. Proceedings of the National Academy of Sciences, USA 110, E2792-E2801.
Filichkin SA, Priest HD, Givan SA, Shen R, Bryant DW, Fox SE, Wong W-K, Mockler TC. 2010. Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Research 20, 45-58.
Fukao Y, Ferjani A, Tomioka R, Nagasaki N, Kurata R, Nishimori Y, Fujiwara M, Maeshima M. 2011. iTRAQ analysis reveals mechanisms of growth defects due to excess zinc in Arabidopsis. Plant Physiology 155, 1893-1907.
Green LS, Rogers EE. 2004. FRD3 controls iron localization in Arabidopsis. Plant Physiology 136, 2523-2531.
Gutiérrez RA, Ewing RM, Cherry JM, Green PJ. 2002. Identification of unstable transcripts in Arabidopsis by cDNA microarray analysis: rapid decay is associated with a group of touch-and specific clock-controlled genes. Proceedings of the National Academy of Sciences, USA 99, 11513-11518.
Hanikenne M, Kroymann J, Trampczynska A, Bernal M, Motte P, Clemens S, Krämer U. 2013. Hard selective sweep and ectopic gene conversion in a gene cluster affording environmental adaptation. PLoS Genetics 9, e1003707.
Hanikenne M, Nouet C. 2011. Metal hyperaccumulation and hypertolerance: a model for plant evolutionary genomics. Current Opinion in Plant Biology 14, 252-259.
Hanikenne M, Talke IN, Haydon MJ, Lanz C, Nolte A, Motte P, Kroymann J, Weigel D, Krämer U. 2008. Evolution of metal hyperaccumulation required cis-regulatory changes and triplication of HMA4. Nature 453, 391-395.
Ito T, Sakai H, Meyerowitz EM. 2003. Whorl-specific expression of the SUPERMAN gene of Arabidopsis is mediated by cis elements in the transcribed region. Current Biology 13, 1524-1530.
Jefferson RA, Kavanagh TA, Bevan MW. 1987. GUS fusions: β-glucuronidase as a sensitive and versatile gene fusion marker in higher plants. EMBO Journal 6, 3901-3907.
Kawaguchi R, Bailey-Serres J. 2005. mRNA sequence features that contribute to translational regulation in Arabidopsis. Nucleic Acids Research 33, 955-965.
Kim Y, Lee G, Jeon E, Sohn Ej, Lee Y, Kang H, Lee Dw, Kim DH, Hwang I. 2014. The immediate upstream region of the 5′-UTR from the AUG start codon has a pronounced effect on the translational efficiency in Arabidopsis thaliana. Nucleic Acids Research 42, 485-498.
Krämer U. 2005. MTP1 mops up excess zinc in Arabidopsis cells. Trends in Plant Science 10, 313-315.
Krämer U. 2010. Metal hyperaccumulation in plants. Annual Review of Plant Biology 61, 517-534.
Krämer U, Talke IN, Hanikenne M. 2007. Transition metal transport. FEBS Letters 581, 2263-2272.
Lin YF, Liang HM, Yang SY, Boch A, Clemens S, Chen CC, Wu JF, Huang JL, Yeh KC. 2009. Arabidopsis IRT3 is a zinc-regulated and plasma membrane localized zinc/iron transporter. New Phytologist 182, 392-404.
Liu M-J, Wu S-H, Chen H-M, Wu S-H. 2012. Widespread translational control contributes to the regulation of Arabidopsis photomorphogenesis. Molecular Systems Biology 8, 566.
Ma X, Li-Ling J, Huang Q, Chen X, Hou L, Ma F. 2009. Systematic analysis of alternative promoters correlated with alternative splicing in human genes. Genomics 93, 420-425.
Mendoza-Cozatl DG, Butko E, Springer F, Torpey JW, Komives EA, Kehr J, Schroeder JI. 2008. Identification of high levels of phytochelatins, glutathione and cadmium in the phloem sap of Brassica napus. A role for thiol-peptides in the long-distance transport of cadmium and the effect of cadmium on iron translocation. The Plant Journal 54, 249-259.
Narsai R, Howell KA, Millar AH, OToole N, Small I, Whelan J. 2007. Genome-wide analysis of mRNA decay rates and their determinants in Arabidopsis thaliana. The Plant Cell 19, 3418-3436.
Nouet C, Motte P, Hanikenne M. 2011. Chloroplastic and mitochondrial metal homeostasis. Trends in Plant Science 16, 395-404.
Palmer CM, Guerinot ML. 2009. Facing the challenges of Cu, Fe and Zn homeostasis in plants. Nature Chemical Biology 5, 333-340.
Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. 2008. Deep surveying of alternative splicing complexity in the human transcriptome by highthroughput sequencing. Nature Genetics 40, 1413-1415.
Petit JM, van Wuytswinkel O, Briat JF, Lobréaux S. 2001. Characterization of an iron-dependent regulatory sequence involved in the transcriptional control of AtFer1 and ZmFer1 plant ferritin genes by iron. Journal of Biological Chemistry 276, 5584-5590.
Pichon X, Wilson LA, Stoneley M, Bastide A, King HA, Somers J, Willis AE. 2012. RNA binding protein/RNA element interactions and the control of translation. Current Protein and Peptide Science 13, 294-304.
Pineau C, Loubet S, Lefoulon C, Chalies C, Fizames C, Lacombe B, Ferrand M, Loudet O, Berthomieu P, Richard O. 2012. Natural variation at the FRD3 MATE transporter locus reveals cross-talk between Fe homeostasis and Zn tolerance in Arabidopsis thaliana. PLoS Genetics 8, e1003120.
Rausin G, Tillemans V, Stankovic N, Hanikenne M, Motte P. 2010. Dynamic nucleocytoplasmic shuttling of an Arabidopsis SR splicing factor: role of the RNA-binding domains. Plant Physiology 153, 273-284.
Ravet K, Reyt G, Arnaud N, Krouk G, Djouani E-B, Boucherez J, Briat J-F, Gaymard F. 2012. Iron and ROS control of the DownSTream mRNA decay pathway is essential for plant fitness. EMBO Journal 31, 175-186.
Rellán-Alvarez R, Giner-Martínez-Sierra J, Orduna J, Orera I, Rodríguez-Castrillón JA, García-Alonso JI, Abadía J, Alvarez-Fernández A. 2010. Identification of a tri-iron(III), tri-citrate complex in the xylem sap of iron-deficient tomato resupplied with iron: new insights into plant iron long-distance transport. Plant and Cell Physiology 51, 91-102.
Remy E, Cabrito TR, Batista RA, Hussein MAM, Teixeira MC, Athanasiadis A, Sá-Correia I, Duque P. 2014. Intron retention in the 5?UTR of the novel ZIF2 transporter enhances translation to promote zinc tolerance in Arabidopsis. PLoS Genetics 10, e1004375.
Richard O, Pineau C, Loubet S, Chalies C, Vile D, Marques L, Berthomieu P. 2011. Diversity analysis of the response to Zn within the Arabidopsis thaliana species revealed a low contribution of Zn translocation to Zn tolerance and a new role for Zn in lateral root development. Plant, Cell, & Environment 34 1065-1078.
Rogers EE, Guerinot ML. 2002. FRD3, a member of the multidrug and toxin efflux family, controls iron deficiency responses in Arabidopsis. The Plant Cell 14, 1787-1799.
Roschzttardtz H, Seguela-Arnaud M, Briat JF, Vert G, Curie C. 2011. The FRD3 citrate effluxer promotes iron nutrition between symplastically disconnected tissues throughout Arabidopsis development. The Plant Cell 23, 2725-2737.
Roux C, Castric V, Pauwels M, Wright SI, Saumitou-Laprade P, Vekemans X. 2011. Does speciation between Arabidopsis halleri and Arabidopsis lyrata coincide with major changes in a molecular target of adaptation? PLoS ONE 6, e26872.
Sato K, Hamada M, Asai K, Mituyama T. 2009. CentroidFold: a web server for RNA secondary structure prediction. Nucleic Acids Research 37, W277-W280.
Schuler M, Rellán-lvarez R, Fink-Straube C, Abadía J, Bauer P. 2012. Nicotianamine functions in the phloem-based transport of iron to sink organs, in pollen development and pollen tube growth in Arabidopsis. The Plant Cell 24, 2380-2400.
Shabalina S, Spiridonov A, Spiridonov N, Koonin E. 2010. Connections between alternative transcription and alternative splicing in mammals. Genome Biology and Evolution 2, 791-799.
Shahzad Z, Gosti F, Frérot H, Lacombe E, Roosens N, Saumitou-Laprade P, Berthomieu P. 2010. The five AhMTP1 zinc transporters undergo different evolutionary fates towards adaptive evolution to zinc tolerance in Arabidopsis halleri. PLoS Genetics 6, e1000911.
Shanmugam V, Lo JC, Wu CL, Wang SL, Lai CC, Connolly EL, Huang JL, Yeh KC. 2011. Differential expression and regulation of iron-regulated metal transporters in Arabidopsis halleri and Arabidopsis thaliana-the role in zinc tolerance. New Phytologist 190, 125-137.
Shanmugam V, Lo J-C, Yeh K-C. 2013. Control of Zn uptake in Arabidopsis halleri: a balance between Zn and Fe. Frontiers in Plant Science 4, 281.
Talke IN, Hanikenne M, Krämer U. 2006. Zinc-dependent global transcriptional control, transcriptional deregulation, and higher gene copy number for genes in metal homeostasis of the hyperaccumulator Arabidopsis halleri. Plant Physiology 142, 148-167.
Tanaka T, Koyanagi KO, Itoh T. 2009. Highly diversified molecular evolution of downstream transcription start sites in rice and Arabidopsis. Plant Physiology 149, 1316-1324.
Verbruggen N, Hermans C, Schat H. 2009. Molecular mechanisms of metal hyperaccumulation in plants. New Phytologist 181, 759-776.
Willems G, Dräger DB, Courbot M, Gode C, Verbruggen N, Saumitou-Laprade P. 2007. The genetic basis of zinc tolerance in the metallophyte Arabidopsis halleri ssp. halleri (Brassicaceae): an analysis of quantitative trait loci. Genetics 176, 659-674.
Yogeeswaran K, Frary A, York TL, Amenta A, Lesser AH, Nasrallah JB, Tanksley SD, Nasrallah ME. 2005. Comparative genome analyses of Arabidopsis spp.: inferring chromosomal rearrangement events in the evolutionary history of A. thaliana. Genome Research 15, 505-515.