Identification and characterization of phosphate transporter genes in potato.

Phosphate transporter (PHTs) have important roles in Pi acquisition, allocation, and signal transduction. The aim of this study is to provide a comprehensive knowledge of PHTs in potato. Very strict homology search and subsequent domain verification using Hidden Markov Models revealed that the potato genome has 20 StPHT and StPHOs genes which were grouped into 5 phylogenetical clusters including 8 PHT1 homologs,1 PHT2 homolog, 2 PHT3 homologs, 5 PHT4 homologs and 4 PHO homologs. These genes were mapped on ten S. tuberosum chromosomes (chr1-9 and 12). Analysis of these genes led to identification of 20 conserved motifs and location prediction showed that PHT1 and PHT4 proteins have 12 transmembrane (TM) domains, PHT2 proteins have 13 TM domains, PHT3 proteins contain 4-5 TM domains, and PHO proteins contain 8-10 TM domains. Two tandem and 2 segmental duplications were further identified from these genes. RT-qPCR analysis showed that most of PHTs and PHOs displayed specific expression patterns with respect to phosphate status, fourteen transporters were up regulated in leaves and 11 transporters were up regulated in roots under phosphate deprivation. StPHT2;1 was found to be expressed both in potato leaf and root after phosphate starvation. Most cis-regulatory elements in StPHTs and StPHOs were found associated with light, defense, stress and hormones responsiveness, endosperm and meristem expression, as well as circadian control. A scan of the coding sequences of 20 StPHTs and StPHOs against published miRNAs in potato predicted a total of 2 potential miRNAs, mainly targeting members located on the same chromosome. Expression of StPHTs and StPHOs was selectively induced by biotic and abiotic stresses, and phytohormone treatments, among them, heat stress exclusively caused the up-regulation of 14 StPHT and StPHO genes, in particular PHO1 members. Most of StPHTs and StPHOs do not exhibit the tissue-specific expression. StPHT1;7, StPHT3;1 and StPHTO1;1 were highly expressed in the root of S. tuberosum, especially the gene StPHT3;1 are highly expressed in 14 tissues which covering the entire life cycle of potato. Our results provide comprehensive insights into the PHT and PHO family genes involved in the growth, development, and stress response of the potato.

[1]  Gerald A. Tuskan,et al.  Divergence of the Dof Gene Families in Poplar, Arabidopsis, and Rice Suggests Multiple Modes of Gene Evolution after Duplication1[W] , 2006, Plant Physiology.

[2]  Shi Shu-li.  Function of Phosphate Transporter OsPHT2; 1 in Improving Phosphate Utilization in Rice , 2013 .

[3]  A. Murphy,et al.  Evolution of transporters in plants , 2014 .

[4]  E. Młodzińska,et al.  Phosphate Uptake and Allocation – A Closer Look at Arabidopsis thaliana L. and Oryza sativa L. , 2016, Front. Plant Sci..

[5]  H. Marschner.  Mineral Nutrition of Higher Plants , 1988 .

[6]  Y. Poirier,et al.  Expression analyses of three members of the AtPHO1 family reveal differential interactions between signaling pathways involved in phosphate deficiency and the responses to auxin, cytokinin, and abscisic acid , 2008, Planta.

[7]  Mingjun Li,et al.  Genomic Identification and Expression Analysis of the Phosphate Transporter Gene Family in Poplar , 2016, Front. Plant Sci..

[8]  W. Terzaghi,et al.  Light-Regulated Transcription , 1995 .

[9]  L. Nussaume,et al.  Phosphate Import in Plants: Focus on the PHT1 Transporters , 2011, Front. Plant Sci..

[10]  K. Shinozaki,et al.  The transcriptional regulatory network in the drought response and its crosstalk in abiotic stress responses including drought, cold, and heat , 2014, Front. Plant Sci..

[11]  G. Finazzi,et al.  Ions channels/transporters and chloroplast regulation. , 2015, Cell calcium.

[12]  Q. Shen,et al.  Involvement of OsPht1;4 in phosphate acquisition and mobilization facilitates embryo development in rice. , 2015, The Plant journal : for cell and molecular biology.

[13]  Bo Hu,et al.  GSDS 2.0: an upgraded gene feature visualization server , 2014, Bioinform..

[14]  D. Schemske,et al.  PATHWAYS, MECHANISMS, AND RATES OF POLYPLOID FORMATION IN FLOWERING PLANTS , 1998 .

[15]  S. Tyerman,et al.  Channel-Like Characteristics of the Low-Affinity Barley Phosphate Transporter PHT1;6 When Expressed in Xenopus Oocytes1[W][OA] , 2010, Plant Physiology.

[16]  Li Liu,et al.  W-box and G-box elements play important roles in early senescence of rice flag leaf , 2016, Scientific Reports.

[17]  M. Nam,et al.  Increased expression of OsPT1, a high-affinity phosphate transporter, enhances phosphate acquisition in rice , 2008, Biotechnology Letters.

[18]  Arne Elofsson,et al.  The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides , 2015, Nucleic Acids Res..

[19]  S. Harashima,et al.  The PHO84 gene of Saccharomyces cerevisiae encodes an inorganic phosphate transporter , 1991, Molecular and cellular biology.

[20]  T. Boller,et al.  Plant phosphorus acquisition in a common mycorrhizal network: regulation of phosphate transporter genes of the Pht1 family in sorghum and flax. , 2015, The New phytologist.

[21]  I. Chung,et al.  Molecular cloning and characterization of a tobacco leaf cDNA encoding a phosphate transporter. , 2001, Molecules and cells.

[22]  A. Osbourn,et al.  Comparative transcriptomics of rice reveals an ancient pattern of response to microbial colonization , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[23]  Q. Cui,et al.  Principles of microRNA regulation of a human cellular signaling network , 2006, Molecular systems biology.

[24]  Guodong Yang,et al.  The Mitochondrial Phosphate Transporters Modulate Plant Responses to Salt Stress via Affecting ATP and Gibberellin Metabolism in Arabidopsis thaliana , 2012, PloS one.

[25]  J. Jansa,et al.  A phosphate transporter expressed in arbuscule-containing cells in potato , 2001, Nature.

[26]  M. J. Harrison,et al.  Closely Related Members of the Medicago truncatula PHT1 Phosphate Transporter Gene Family Encode Phosphate Transporters with Distinct Biochemical Activities* , 2008, Journal of Biological Chemistry.

[27]  F. Smith.  Sulphur and phosphorus transport systems in plants , 2002 .

[28]  W. Versaw,et al.  Differential expression and phylogenetic analysis suggest specialization of plastid-localized members of the PHT4 phosphate transporter family for photosynthetic and heterotrophic tissues , 2008, Plant signaling & behavior.

[29]  M. Bucher.  Functional biology of plant phosphate uptake at root and mycorrhiza interfaces. , 2007, The New phytologist.

[30]  Pablo Librado,et al.  DnaSP v5: a software for comprehensive analysis of DNA polymorphism data , 2009, Bioinform..

[31]  C. Spetea,et al.  The Sink-Specific Plastidic Phosphate Transporter PHT4;2 Influences Starch Accumulation and Leaf Size in Arabidopsis1[W][OA] , 2011, Plant Physiology.

[32]  Y. Poirier,et al.  Structure and Expression Profile of the Arabidopsis PHO1 Gene Family Indicates a Broad Role in Inorganic Phosphate Homeostasis1[w] , 2004, Plant Physiology.

[33]  Chris Somerville,et al.  Identification and Characterization of the Arabidopsis PHO1 Gene Involved in Phosphate Loading to the Xylem Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.000745. , 2002, The Plant Cell Online.

[34]  L. Herrera-Estrella,et al.  Phosphate nutrition: improving low-phosphate tolerance in crops. , 2014, Annual review of plant biology.

[35]  Z. Gu,et al.  Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. , 2002, Molecular biology and evolution.

[36]  D. De Koeyer,et al.  Differences between the Bud End and Stem End of Potatoes in Dry Matter Content, Starch Granule Size, and Carbohydrate Metabolic Gene Expression at the Growing and Sprouting Stages. , 2016, Journal of agricultural and food chemistry.

[37]  Xin-ping Chen,et al.  Genome-wide Identification, Characterization, and Expression Analysis of PHT1 Phosphate Transporters in Wheat , 2017, Front. Plant Sci..

[38]  Jun Li,et al.  KaKs_Calculator: Calculating Ka and Ks Through Model Selection and Model Averaging , 2007, Genom. Proteom. Bioinform..

[39]  S. Baldwin,et al.  Phosphate Concentration and Arbuscular Mycorrhizal Colonisation Influence the Growth, Yield and Expression of Twelve PHT1 Family Phosphate Transporters in Foxtail Millet (Setaria italica) , 2014, PloS one.

[40]  M. J. Harrison,et al.  Phosphate transport in Arabidopsis: Pht1;1 and Pht1;4 play a major role in phosphate acquisition from both low- and high-phosphate environments. , 2004, The Plant journal : for cell and molecular biology.

[41]  Wei Wang,et al.  Systematic Identification, Evolution and Expression Analysis of the Zea mays PHT1 Gene Family Reveals Several New Members Involved in Root Colonization by Arbuscular Mycorrhizal Fungi , 2016, International journal of molecular sciences.

[42]  I. Somssich,et al.  Synthetic Plant Promoters Containing Defined Regulatory Elements Provide Novel Insights into Pathogen- and Wound-Induced Signaling Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.010412. , 2002, The Plant Cell Online.

[43]  T. Sugiyama,et al.  Isolation and characterization of cDNAs encoding mitochondrial phosphate transporters in soybean, maize, rice, and Arabidopsis , 1999, Plant Molecular Biology.

[44]  A. Miller,et al.  TRANSPORTERS RESPONSIBLE FOR THE UPTAKE AND PARTITIONING OF NITROGENOUS SOLUTES. , 2001, Annual review of plant physiology and plant molecular biology.

[45]  Xingming Lian,et al.  Comprehensive sequence and whole-life-cycle expression profile analysis of the phosphate transporter gene family in rice. , 2011, Molecular plant.

[46]  Songnian Hu,et al.  EvolView, an online tool for visualizing, annotating and managing phylogenetic trees , 2012, Nucleic Acids Res..

[47]  S. Baldwin,et al.  Replace, reuse, recycle: improving the sustainable use of phosphorus by plants. , 2015, Journal of experimental botany.

[48]  Ruibo Hu,et al.  The pattern of Phosphate transporter 1 genes evolutionary divergence in Glycine max L. , 2013, BMC Plant Biology.

[49]  D. Eastwood,et al.  Changes in Gene Expression in Arabidopsis Shoots during Phosphate Starvation and the Potential for Developing Smart Plants1 , 2003, Plant Physiology.

[50]  R. Jost,et al.  Arabidopsis PHOSPHATE TRANSPORTER1 genes PHT1;8 and PHT1;9 are involved in root-to-shoot translocation of orthophosphate , 2014, BMC Plant Biology.

[51]  Y. Poirier,et al.  Phosphate Transport and Homeostasis in Arabidopsis , 2002, The arabidopsis book.

[52]  Sophie Bernard,et al.  Golgi-Mediated Synthesis and Secretion of Matrix Polysaccharides of the Primary Cell Wall of Higher Plants , 2012, Front. Plant Sci..

[53]  Shrikant S. Mantri,et al.  Tissue specific transcript profiling of wheat phosphate transporter genes and its association with phosphate allocation in grains , 2016, Scientific Reports.

[54]  Shubin Sun,et al.  A Constitutive Expressed Phosphate Transporter, OsPht1;1, Modulates Phosphate Uptake and Translocation in Phosphate-Replete Rice1[W][OA] , 2012, Plant Physiology.

[55]  F. W. Smith,et al.  Characterization of two phosphate transporters from barley; evidence for diverse function and kinetic properties among members of the Pht1 family , 2003, Plant Molecular Biology.

[56]  P. Jiang,et al.  Roles, Regulation, and Agricultural Application of Plant Phosphate Transporters , 2017, Front. Plant Sci..

[57]  S. Shiu,et al.  Evolutionary Relationships and Functional Diversity of Plant Sulfate Transporters , 2011, Front. Plant Sci..

[58]  C. Rausch,et al.  Molecular mechanisms of phosphate transport in plants , 2002, Planta.

[59]  Turgay Unver,et al.  Regulation of the alkaloid biosynthesis by miRNA in opium poppy. , 2015, Plant biotechnology journal.

[60]  S. Pradervand,et al.  The EXS Domain of PHO1 Participates in the Response of Shoots to Phosphate Deficiency via a Root-to-Shoot Signal1[OPEN] , 2015, Plant Physiology.

[61]  Mostafa Ahmadizadeh,et al.  In Silico Analysis of Cis-Regulatory Elements on Co-Expressed Genes , 2015 .

[62]  K. Shinozaki,et al.  DNA-binding domains of plant-specific transcription factors: structure, function, and evolution. , 2013, Trends in plant science.

[63]  Chuang Wang,et al.  Rice SPX-Major Facility Superfamily3, a Vacuolar Phosphate Efflux Transporter, Is Involved in Maintaining Phosphate Homeostasis in Rice1[OPEN] , 2015, Plant Physiology.

[64]  Q. Shen,et al.  Two rice phosphate transporters, OsPht1;2 and OsPht1;6, have different functions and kinetic properties in uptake and translocation. , 2009, The Plant journal : for cell and molecular biology.

[65]  D. R. Hoagland,et al.  The Water-Culture Method for Growing Plants Without Soil , 2018 .

[66]  K. Raghothama,et al.  Transcriptional regulation and functional properties of Arabidopsis Pht1;4, a high affinity transporter contributing greatly to phosphate uptake in phosphate deprived plants , 2004, Plant Molecular Biology.

[67]  Aaron P. Smith,et al.  Arabidopsis Pht1;5 Mobilizes Phosphate between Source and Sink Organs and Influences the Interaction between Phosphate Homeostasis and Ethylene Signaling1[W][OA] , 2011, Plant Physiology.

[68]  Kathleen Marchal,et al.  PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences , 2002, Nucleic Acids Res..

[69]  Hao Li,et al.  High-Throughput MicroRNA and mRNA Sequencing Reveals That MicroRNAs May Be Involved in Melatonin-Mediated Cold Tolerance in Citrullus lanatus L. , 2016, Front. Plant Sci..

[70]  K. Raghothama.  Phosphate transport and signaling. , 2000, Current opinion in plant biology.

[71]  M. Wissuwa,et al.  Root hair formation in rice (Oryza sativa L.) differs between root types and is altered in artificial growth conditions. , 2016, Journal of experimental botany.

[72]  S. Baldwin,et al.  The conservation of phosphate-binding residues among PHT1 transporters suggests that distinct transport affinities are unlikely to result from differences in the phosphate-binding site. , 2016, Biochemical Society transactions.

[73]  M. J. Harrison,et al.  A Chloroplast Phosphate Transporter, PHT2;1, Influences Allocation of Phosphate within the Plant and Phosphate-Starvation Responses Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.002220. , 2002, The Plant Cell Online.

[74]  L. Willmitzer,et al.  Two cDNAs from potato are able to complement a phosphate uptake-deficient yeast mutant: identification of phosphate transporters from higher plants. , 1997, The Plant cell.

[75]  L. Nussaume,et al.  Reducing the Genetic Redundancy of Arabidopsis PHOSPHATE TRANSPORTER1 Transporters to Study Phosphate Uptake and Signaling1[OPEN] , 2015, Plant Physiology.

[76]  Xingming Lian,et al.  The Phosphate Transporter Gene OsPht1;4 Is Involved in Phosphate Homeostasis in Rice , 2015, PloS one.

[77]  Patrick Xuechun Zhao,et al.  psRNATarget: a plant small RNA target analysis server , 2011, Nucleic Acids Res..

[78]  J. Nevins.  The pathway of eukaryotic mRNA formation. , 1983, Annual review of biochemistry.

[79]  V. Rubio,et al.  Influence of cytokinins on the expression of phosphate starvation responsive genes in Arabidopsis. , 2000, The Plant journal : for cell and molecular biology.

[80]  Steven B Cannon,et al.  The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana , 2004, BMC Plant Biology.

[81]  J. Messing,et al.  Plant Gene Structure , 1983 .

[82]  Wilfred W. Li,et al.  MEME: discovering and analyzing DNA and protein sequence motifs , 2006, Nucleic Acids Res..

[83]  Shubin Sun,et al.  Genome-wide investigation and expression analysis suggest diverse roles and genetic redundancy of Pht1 family genes in response to Pi deficiency in tomato , 2014, BMC Plant Biology.

[84]  K. Raghothama,et al.  Phosphate transporters from the higher plant Arabidopsis thaliana. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[85]  B. Usadel,et al.  Genome-wide reprogramming of metabolism and regulatory networks of Arabidopsis in response to phosphorus. , 2007, Plant, cell & environment.

[86]  O. Voinnet,et al.  Roles of plant small RNAs in biotic stress responses. , 2009, Annual review of plant biology.

[87]  F. W. Smith,et al.  Expression analysis suggests novel roles for members of the Pht1 family of phosphate transporters in Arabidopsis. , 2002, The Plant journal : for cell and molecular biology.

[88]  T. Davies,et al.  Restricted spatial expression of a high-affinity phosphate transporter in potato roots , 2003, Journal of Cell Science.

[89]  David M. Goodstein,et al.  Phytozome: a comparative platform for green plant genomics , 2011, Nucleic Acids Res..

[90]  Arnaud Baumann,et al.  Characterization of the Rice PHO1 Gene Family Reveals a Key Role for OsPHO1;2 in Phosphate Homeostasis and the Evolution of a Distinct Clade in Dicotyledons1[C][W][OA] , 2010, Plant Physiology.

[91]  P. Hasegawa,et al.  The phosphate transporter PHT4;6 is a determinant of salt tolerance that is localized to the Golgi apparatus of Arabidopsis. , 2009, Molecular plant.

[92]  A. Karthikeyan,et al.  Regulated Expression of Arabidopsis Phosphate Transporters1 , 2002, Plant Physiology.

[93]  Cole Trapnell,et al.  Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.

[94]  David M. A. Martin,et al.  Genome sequence and analysis of the tuber crop potato , 2011, Nature.

[95]  E. Blancaflor,et al.  Functional analysis of the Arabidopsis PHT4 family of intracellular phosphate transporters. , 2008, The New phytologist.

[96]  U. Paszkowski,et al.  Rice phosphate transporters include an evolutionarily divergent gene specifically activated in arbuscular mycorrhizal symbiosis , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[97]  F. Skoog,et al.  A revised medium for rapid growth and bio assays with tobacco tissue cultures , 1962 .

[98]  Xuemei Chen,et al.  Small RNAs and their roles in plant development. , 2009, Annual review of cell and developmental biology.

[99]  E. Lam,et al.  ASF-2: a factor that binds to the cauliflower mosaic virus 35S promoter and a conserved GATA motif in Cab promoters. , 1989, The Plant cell.

[100]  Y. Poirier,et al.  Coordination between zinc and phosphate homeostasis involves the transcription factor PHR1, the phosphate exporter PHO1, and its homologue PHO1;H3 in Arabidopsis , 2014, Journal of experimental botany.