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Genome-wide exploration of metal tolerance protein (MTP) genes in common wheat (Triticum aestivum): insights into metal homeostasis and biofortification

Abstract

Metal transport process in plants is a determinant of quality and quantity of the harvest. Although it is among the most important of staple crops, knowledge about genes that encode for membrane-bound metal transporters is scarce in wheat. Metal tolerance proteins (MTPs) are involved in trace metal homeostasis at the sub-cellular level, usually by providing metal efflux out of the cytosol. Here, by using various bioinformatics approaches, genes that encode for MTPs in the hexaploid wheat genome (Triticum aestivum, abbreviated as Ta) were identified and characterized. Based on the comparison with known rice MTPs, the wheat genome contained 20 MTP sequences; named as TaMTP1–8A, B and D. All TaMTPs contained a cation diffusion facilitator (CDF) family domain and most members harbored a zinc transporter dimerization domain. Based on motif, phylogeny and alignment analysis, A, B and D genomes of TaMTP3–7 sequences demonstrated higher homology compared to TaMTP1, 2 and 8. With reference to their rice orthologs, TaMTP1s and TaMTP8s belonged to Zn-CDFs, TaMTP2s to Fe/Zn-CDFs and TaMTP3–7s to Mn-CDFs. Upstream regions of TaMTP genes included diverse cis-regulatory motifs, indicating regulation by developmental stage, tissue type and stresses. A scan of the coding sequences of 20 TaMTPs against published miRNAs predicted a total of 14 potential miRNAs, mainly targeting the members of most diverged groups. Expression analysis showed that several TaMTPs were temporally and spatially regulated during the developmental time-course. In grains, MTPs were preferentially expressed in the aleurone layer, which is known as a reservoir for high concentrations of iron and zinc. The work identified and characterized metal tolerance proteins in common wheat and revealed a potential involvement of MTPs in providing a sink for trace element storage in wheat grains.

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References

  • Arrivault S, Senger T, Krämer U (2006) The Arabidopsis metal tolerance protein AtMTP3 maintains metal homeostasis by mediating Zn exclusion from the shoot under Fe deficiency and Zn oversupply. Plant J 46(5):861–879

    CAS  Article  PubMed  Google Scholar 

  • Bae SH, Han HW, Moon J (2015) Functional analysis of the molecular interactions of TATA box-containing genes and essential genes. PLoS ONE 10(3):e0120848

    Article  PubMed  PubMed Central  Google Scholar 

  • Borg S, Brinch-Pedersen H, Tauris B, Holm PB (2009) Iron transport, deposition and bioavailability in the wheat and barley grain. Plant Soil 325(1–2):15–24

    CAS  Article  Google Scholar 

  • Brenchley R, Spannagl M, Pfeifer M, Barker GL, D’Amore R, Allen AM, Kay S (2012) Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature 491(7426):705–710

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Bailey TL, Boden M, Buske, FA, Frith M, Grant, CE, Clementi L & Noble WS (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res, gkp335

  • Cannon SB, Mitra A, Baumgarten A, Young ND, May G (2004) The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biol 4(1):1

    Article  Google Scholar 

  • Chen L, Liu YG (2014) Male sterility and fertility restoration in crops. Annu Rev Plant Biol 65:579–606

    CAS  Article  PubMed  Google Scholar 

  • Chen Z, Li F, Yang S, Dong Y, Yuan Q, Wang F, Pei X (2013a) Identification and functional analysis of flowering related microRNAs in common wild rice (Oryza rufipogon Griff.). PLoS ONE 8(12):e82844

    Article  PubMed  PubMed Central  Google Scholar 

  • Chen Z et al (2013b) Mn tolerance in rice is mediated by MTP8. 1, a member of the cation diffusion facilitator family. J Exp Bot 64(14):4375–4387

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Choulet F, Alberti A, Theil S, Glover N, Barbe V, Daron J, Leroy P (2014) Structural and functional partitioning of bread wheat chromosome 3B. Science 345(6194):1249721

    Article  PubMed  Google Scholar 

  • Clemens S, Palmgren MG, Krämer U (2002) A long way ahead: understanding and engineering plant metal accumulation. Trends Plant Sci 7(7):309–315

    CAS  Article  PubMed  Google Scholar 

  • Cubillas C, Vinuesa P, Tabche ML, García-de los Santos A (2013) Phylogenomic analysis of cation diffusion facilitator proteins uncovers Ni2+/Co2+ transporters. Metallomics 5(12):1634–1643

    CAS  Article  PubMed  Google Scholar 

  • Cui Q, Yu Z, Purisima EO, Wang E (2006) Principles of microRNA regulation of a human cellular signaling network. Mol Syst Biol 2(1):46

    PubMed  PubMed Central  Google Scholar 

  • Dai X, Zhao PX (2011) psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 39(suppl 2):W155–W159

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Das N et al (2016) Enhanced cadmium accumulation and tolerance in transgenic tobacco overexpressing rice metal tolerance protein gene OsMTP1 is promising for phytoremediation. Plant Physiol Biochem 105:297–309

    CAS  Article  PubMed  Google Scholar 

  • Delhaize E, Gruber BD, Pittman JK, White RG, Leung H, Miao Y, Richardson AE (2007) A role for the AtMTP11 gene of Arabidopsis in manganese transport and tolerance. Plant J 51(2):198–210

    CAS  Article  PubMed  Google Scholar 

  • Eroglu S (2015) Characterization of MTP8 as a tonoplast Fe/Mn transporter essential for Fe efficiency and for Fe and Mn localization in the subepidermis of Arabidopsis embryos (Doctoral dissertation, Halle (Saale), Universitäts-und Landesbibliothek Sachsen-Anhalt, Diss., 2015)

  • Eroglu S, Meier B, von Wirén N, Peiter E (2016) The vacuolar manganese transporter MTP8 determines tolerance to iron deficiency-induced chlorosis in Arabidopsis. Plant Physiol 170(2):1030–1045

    CAS  Article  PubMed  Google Scholar 

  • Fujiwara T, Kawachi M, Sato Y, Mori H, Kutsuna N, Hasezawa S, Maeshima M (2015) A high molecular mass zinc transporter MTP12 forms a functional heteromeric complex with MTP5 in the Golgi in Arabidopsis thaliana. FEBS J 282(10):1965–1979

    CAS  Article  PubMed  Google Scholar 

  • Gu Z, Cavalcanti A, Chen FC, Bouman P, Li WH (2002) Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. Mol Biol Evol 19(3):256–262

    CAS  Article  PubMed  Google Scholar 

  • Gu M, Xu K, Chen A, Zhu Y, Tang G, Xu G (2010) Expression analysis suggests potential roles of microRNAs for phosphate and arbuscular mycorrhizal signaling in Solanum lycopersicum. Physiol Plant 138(2):226–237

    CAS  Article  PubMed  Google Scholar 

  • Gustin JL, Zanis MJ, Salt DE (2011) Structure and evolution of the plant cation diffusion facilitator family of ion transporters. BMC Evol Biol 11(1):1

    Article  Google Scholar 

  • Hall T (2011) BioEdit: an important software for molecular biology. GERF Bull Biosci 2(1):6

    Google Scholar 

  • International Wheat Genome Sequencing Consortium (2014) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345(6194):1251788

    Article  Google Scholar 

  • Jin Q, Xue Z, Dong C, Wang Y, Chu L, Xu Y (2015) Identification and characterization of microRNAs from tree peony (Paeonia ostii) and their response to copper stress. PLoS ONE 10(2):e0117584

    Article  PubMed  PubMed Central  Google Scholar 

  • Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJ (2015) The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc 10(6):845–858

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Kim SA, Punshon T, Lanzirotti A, Li L, Alonso JM, Ecker JR, Kaplan J, Guerinot ML (2006) Localization of iron in Arabidopsis seed requires the vacuolar membrane transporter VIT1. Science 314(5803):1295–1298

    CAS  Article  PubMed  Google Scholar 

  • Kinsella RJ, Kähäri A, Haider S, Zamora J, Proctor G, Spudich G & Kersey P (2011) Ensembl BioMarts: a hub for data retrieval across taxonomic space. Database, bar030

  • Kircher S, Ledger S, Hayashi H, Weisshaar B, Schäfer E, Frohnmeyer H (1998) CPRF4a, a novel plant bZIP protein of the CPRF family: comparative analyses of light- dependent expression, post-transcriptional regulation, nuclear import and heterodimerisation. Mol Gen Genet MGG 257(6):595–605

    CAS  Article  PubMed  Google Scholar 

  • Kobae Y, Uemura T, Sato MH, Ohnishi M, Mimura T, Nakagawa T, Maeshima M (2004) Zinc transporter of Arabidopsis thaliana AtMTP1 is localized to vacuolar membranes and implicated in zinc homeostasis. Plant Cell Physiol 45(12):1749–1758

    CAS  Article  PubMed  Google Scholar 

  • Kolaj-Robin O, Russell D, Hayes KA, Pembroke JT, Soulimane T (2015) Cation diffusion facilitator family: structure and function. FEBS Lett 589(12):1283–1295

    CAS  Article  PubMed  Google Scholar 

  • Kumar R (2014) Role of microRNAs in biotic and abiotic stress responses in crop plants. Appl Biochem Biotechnol 174(1):93–115

    CAS  Article  PubMed  Google Scholar 

  • Laloum T, De Mita S, Gamas P, Baudin M, Niebel A (2013) CCAAT-box binding transcription factors in plants: y so many? Trends Plant Sci 18(3):157–166

    CAS  Article  PubMed  Google Scholar 

  • Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, Rombauts S (2002) PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res 30(1):325–327

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Liang G Ai Q, Yu D (2015) Uncovering miRNAs involved in crosstalk between nutrient deficiencies in Arabidopsis. Sci Rep, 5

  • Liu L, Xu W, Hu X, Liu H, Lin, Y (2016) W-box and G-box elements play important roles in early senescence of rice flag leaf. Sci Rep, 6

  • Lovell SC, Davis IW, Arendall WB, de Bakker PI, Word JM, Prisant MG, Richardson DC (2003) Structure validation by Cα geometry: ϕ, ψ and Cβ deviation. Proteins Struct Funct Bioinformat 50(3):437–450

    CAS  Google Scholar 

  • Lu M, Fu D (2007) Structure of the zinc transporter YiiP. Science 317(5845):1746–1748

    CAS  Article  PubMed  Google Scholar 

  • Lu M, Chai J, Fu D (2009) Structural basis for autoregulation of the zinc transporter YiiP. Nat Struct Mol Biol 16(10):1063–1067

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Lv S, Nie X, Wang L, Du X, Biradar SS, Jia X, Weining S (2012) Identification and characterization of microRNAs from barley (Hordeum vulgare L.) by high-throughput sequencing. Int J Mol Sci 13(3):2973–2984

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Marcelis LFM (1996) Sink strength as a determinant of dry matter partitioning in the whole plant. J Exp Bot 47:1281–1291

    CAS  Article  PubMed  Google Scholar 

  • Marschner H (2012) Marschner’s mineral nutrition of higher plants, vol 89. Academic press, London

    Google Scholar 

  • Mazzolini AP, Pallaghy CK, Legge GJF (1985) Quantitative microanalysis of Mn, Zn and other elements in mature wheat seed. New Phytol 100(4):483–509

    CAS  Article  Google Scholar 

  • Meng Y, Shao C, Ma X, Wang H, Chen M (2012) Expression-based functional investigation of the organ-specific microRNAs in Arabidopsis. PLoS ONE 7(11):e50870

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Menguer PK, Farthing E, Peaston KA, Ricachenevsky FK, Fett JP, Williams LE (2013). Functional analysis of the rice vacuolar zinc transporter OsMTP1. J Exp Bot 64(10):2871–2883

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Montanini B, Blaudez D, Jeandroz S, Sanders D, Chalot M (2007) Phylogenetic and functional analysis of the Cation Diffusion Facilitator (CDF) family: improved signature and prediction of substrate specificity. BMC Genom 8(1):1

    Article  Google Scholar 

  • Nguyen MN, Tan KP, Madhusudhan MS (2011) CLICK—topology-independent comparison of biomolecular 3D structures. Nucleic Acids Res 39(suppl 2):W24–W28

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Ozyigit II, Filiz E, Vatansever R, Kurtoglu KY, Koc I, Öztürk MX, Anjum NA (2016) Identification and comparative analysis of H2O2-scavenging enzymes (ascorbate peroxidase and glutathione peroxidase) in selected plants employing bioinformatics approaches. Front Plant Sci 7:301

    Article  PubMed  PubMed Central  Google Scholar 

  • Pearce S, Tabbita F, Cantu D, Buffalo V, Avni R, Vazquez-Gross H, Dubcovksy J (2014) Regulation of Zn and Fe transporters by the GPC1 gene during early wheat monocarpic senescence. BMC Plant Biol 14(1):1

    Article  Google Scholar 

  • Pearce S et al (2015) WheatExp: an RNA-seq expression database for polyploid wheat. BMC Plant Biol 15(1):1

    Article  Google Scholar 

  • Peiter E, Montanini B, Gobert A, Pedas P, Husted S, Maathuis FJ, Sanders D (2007) A secretory pathway-localized cation diffusion facilitator confers plant manganese tolerance. Proc Natl Acad Sci USA 104(20):8532–8537

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Pfeifer M, Kugler KG, Sandve SR, Zhan B, Rudi H, Hvidsten TR, International Wheat Genome Sequencing Consortium (2014) Genome interplay in the grain transcriptome of hexaploid bread wheat. Science 345(6194):1250091

    Article  PubMed  Google Scholar 

  • Qu LQ, Yoshihara T, Ooyama A, Goto F, Takaiwa F (2005) Iron accumulation does not parallel the high expression level of ferritin in transgenic rice seeds. Planta 222(2):225–233

    CAS  Article  Google Scholar 

  • Ramsey J, Schemske DW (1998) Pathways, mechanisms, and rates of polyploid formation in flowering plants. Annu Rev Ecol Syst 29:467–501

    Article  Google Scholar 

  • Ravel C, Fiquet S, Boudet J, Dardevet M, Vincent J, Merlino M, Martre P (2015) Conserved cis-regulatory modules in promoters of genes encoding wheat high-molecular- weight glutenin subunits. Adv Seed Biol, 150

  • Regvar M, Eichert D, Kaulich B, Gianoncelli A, Pongrac P, Vogel-Mikuš K, Kreft I (2011) New insights into globoids of protein storage vacuoles in wheat aleurone using synchrotron soft X-ray microscopy. J Exp Bot 62:3929–3939

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Ricachenevsky FK, Menguer PK, Sperotto RA, Williams LE, Fett JP (2013) Roles of plant metal tolerance proteins (MTP) in metal storage and potential use in biofortification strategies. Front Plant Sci 4:144

    PubMed  PubMed Central  Google Scholar 

  • Sze H, Chen LQ, Jez JM (2014) Evolutionary relationships and functional diversity of plant sulfate transporters. Evol Transp Plants, 63

  • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30(12):2725–2729

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Thomine S, Vert G (2013) Iron transport in plants: better be safe than sorry. Curr Opin Plant Biol 16(3):322–327

    CAS  Article  PubMed  Google Scholar 

  • Toledo-Ortiz G, Huq E, Quail PH (2003) The Arabidopsis basic/helix-loop-helix transcription factor family. Plant Cell 15(8):1749–1770

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Uauy C, Distelfeld A, Fahima T, Blechl A, Dubcovsky J (2006) A NAC gene regulating senescence improves grain protein, zinc, and iron content in wheat. Science 314(5803):1298–1301

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  • Ueno D, Sasaki A, Yamaji N, Miyaji T, Fujii Y, Takemoto Y, Ma JF (2015) A polarly localized transporter for efficient manganese uptake in rice. Nature plants 1:15170

    CAS  Article  PubMed  Google Scholar 

  • Vatansever R, Koc I, Ozyigit II, Sen U, Uras ME, Anjum NA, Filiz E (2016) Genome-wide identification and expression analysis of sulfate transporter (SULTR) genes in potato (Solanum tuberosum L.). Planta 244(6):1167–1183

    CAS  Article  PubMed  Google Scholar 

  • White PJ, Broadley MR (2009) Biofortification of crops with seven mineral elements often lacking in human diets–iron, zinc, copper, calcium, magnesium, selenium and iodine. New Phytol 182(1):49–84

    CAS  Article  PubMed  Google Scholar 

  • Xu D, Mou G, Wang K, Zhou G (2014) MicroRNAs responding to southern rice black- streaked dwarf virus infection and their target genes associated with symptom development in rice. Virus Res 190:60–68

    CAS  Article  PubMed  Google Scholar 

  • Xu XW, Li T, Li Y, Li ZX (2015) Identification and analysis of C. annuum microRNAs by high-throughput sequencing and their association with high temperature and high air humidity stress. Int J Bioautom 19:459–472

    Google Scholar 

  • Yamasaki K, Kigawa T, Seki M, Shinozaki K, Yokoyama S (2013) DNA-binding domains of plant-specific transcription factors: structure, function, and evolution. Trends Plant Sci 18(5):267–276

    CAS  Article  PubMed  Google Scholar 

  • Yuan L, Yang S, Liu B, Zhang M, Wu K (2012) Molecular characterization of a rice metal tolerance protein, OsMTP1. Plant Cell Rep 31(1):67–79

    Article  PubMed  Google Scholar 

  • Yuan L, Tang J, Liu J, Song H, Zhang M, Li H, Li C (2016) Differential miRNA expression in maize ear subjected to shading tolerance. Acta Physiol Plant 38(3):1–12

    Article  Google Scholar 

  • Zhang Y, Xu YH, Yi HY, Gong JM (2012) Vacuolar membrane transporters OsVIT1 and OsVIT2 modulate iron translocation between flag leaves and seeds in rice. Plant J 72(3):400–410

    CAS  Article  PubMed  Google Scholar 

  • Zong Y, Huang L, Zhang T, Qin Q, Wang W, Zhao X, Li Z (2014) Differential microRNA expression between shoots and rhizomes in Oryza longistaminata using high- throughput RNA sequencing. The Crop Journal 2(2):102–109

    Article  Google Scholar 

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Acknowledgements

We thank Benjamin Gruber for the fruitful discussion and proofreading of the article. Seckin Eroglu thanks Scientific and Technological Council of Turkey (Ankara, Turkey) for the fellowship through BIDEB-2232 program.

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Correspondence to Seckin Eroglu.

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Vatansever, R., Filiz, E. & Eroglu, S. Genome-wide exploration of metal tolerance protein (MTP) genes in common wheat (Triticum aestivum): insights into metal homeostasis and biofortification. Biometals 30, 217–235 (2017). https://doi.org/10.1007/s10534-017-9997-x

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Keywords

  • CDF
  • Micronutrient
  • Aleurone
  • Deficiency
  • Biofortification