PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT4G28610.1
Common NameAtPHR1, PHR1, T5F17.60
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family G2-like
Protein Properties Length: 409aa    MW: 45546.3 Da    PI: 6.1215
Description phosphate starvation response 1
Gene Model
Gene Model ID Type Source Coding Sequence
AT4G28610.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
      G2-like   1 kprlrWtpeLHerFveaveqLGGsekAtPktilelmkvkgLtlehvkSHLQkYRl 55 
                  k+r+rWtpeLHe+Fveav++LGGse+AtPk +l++mkv+gLt++hvkSHLQkYR+
                  68****************************************************8 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5129411.291222282IPR017930Myb domain
TIGRFAMsTIGR015571.5E-24225279IPR006447Myb domain, plants
PfamPF002494.5E-9227278IPR001005SANT/Myb domain
PfamPF143792.7E-24313356IPR025756MYB-CC type transcription factor, LHEQLE-containing domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0007623Biological Processcircadian rhythm
GO:0016036Biological Processcellular response to phosphate starvation
GO:0055063Biological Processsulfate ion homeostasis
GO:0071486Biological Processcellular response to high light intensity
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
PO:0000084anatomyplant sperm cell
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0008019anatomyleaf lamina base
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009025anatomyvascular leaf
PO:0009052anatomyflower pedicel
PO:0020137anatomyleaf apex
PO:0025022anatomycollective leaf structure
PO:0025195anatomypollen tube cell
PO:0001016developmental stageL mature pollen stage
PO:0001017developmental stageM germinated pollen stage
PO:0001054developmental stagevascular leaf senescent stage
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001081developmental stagemature plant embryo stage
PO:0001185developmental stageplant embryo globular stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007064developmental stageLP.12 twelve leaves visible stage
PO:0007095developmental stageLP.08 eight leaves visible stage
PO:0007098developmental stageLP.02 two leaves visible stage
PO:0007103developmental stageLP.10 ten leaves visible stage
PO:0007115developmental stageLP.04 four leaves visible stage
PO:0007123developmental stageLP.06 six leaves visible stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 409 aa     Download sequence    Send to blast
3D Structure ? help Back to Top
PDB ID Evalue Query Start Query End Hit Start Hit End Description
6j4k_A6e-35224283160Protein PHOSPHATE STARVATION RESPONSE 1
6j4k_B6e-35224283160Protein PHOSPHATE STARVATION RESPONSE 1
6j5b_A6e-35224283160Protein PHOSPHATE STARVATION RESPONSE 1
6j5b_C6e-35224283160Protein PHOSPHATE STARVATION RESPONSE 1
6j5b_D6e-35224283160Protein PHOSPHATE STARVATION RESPONSE 1
6j5b_F6e-35224283160Protein PHOSPHATE STARVATION RESPONSE 1
6j5b_H6e-35224283160Protein PHOSPHATE STARVATION RESPONSE 1
6j5b_J6e-35224283160Protein PHOSPHATE STARVATION RESPONSE 1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.45250.0cell culture| flower| leaf| seed| silique
Expression -- Microarray ? help Back to Top
Source ID E-value
Expression AtlasAT4G28610-
Functional Description ? help Back to Top
Source Description
TAIRSimilar to phosphate starvation response gene from Chlamydomonas. Weakly responsive to phosphate starvation. Acts upstream of PHO2 in phosphate signaling.
UniProtTranscription factor involved in phosphate starvation signaling (PubMed:11511543, PubMed:17927693, PubMed:26586833). Binds as a dimer to P1BS, an imperfect palindromic sequence 5'-GNATATNC-3', to promote the expression of inorganic phosphate (Pi) starvation-responsive genes (PubMed:11511543, PubMed:20838596, PubMed:26586833). SPX1 is a competitive inhibitor of this DNA-binding (PubMed:25271326). PHR1 binding to its targets is low Pi-dependent (PubMed:25271326). Regulates the expression of miR399 (PubMed:20838596). Regulates the expression of IPS1 (At3g09922), a non-coding RNA that mimics the target of miR399 to block the cleavage of PHO2 under Pi-deficient conditions (PubMed:17643101). Regulates lipid remodeling and triacylglycerol accumulation during phosphorus starvation (PubMed:25680792). Required for the shoot-specific hypoxic response (PubMed:24753539). Regulates FER1 expression upon phosphate starvation, linking iron and phosphate homeostasis (PubMed:23788639). Contributes to the homeostasis of both sulfate and phosphate in plants under phosphate deficiency (PubMed:21261953). Required for adaptation to high light and retaining functional photosynthesis during phosphate starvation (PubMed:21910737). Involved in the coregulation of Zn and Pi homeostasis (PubMed:24420568). {ECO:0000269|PubMed:11511543, ECO:0000269|PubMed:17643101, ECO:0000269|PubMed:17927693, ECO:0000269|PubMed:20838596, ECO:0000269|PubMed:21261953, ECO:0000269|PubMed:21910737, ECO:0000269|PubMed:23788639, ECO:0000269|PubMed:24420568, ECO:0000269|PubMed:24753539, ECO:0000269|PubMed:25271326, ECO:0000269|PubMed:25680792, ECO:0000269|PubMed:26586833}.
Function -- GeneRIF ? help Back to Top
  1. In darkness, expression of the PHR1 and UVR3 photolyase genes, responsible for photoreactivation, is maintained at a basal level through the positive action of HY5 and HYH photomorphogenesis-promoting transcription factors
    [PMID: 20487384]
  2. PHR1 and PHL1 are partially redundant transcription factors acting as central integrators of phosphate starvation responses.
    [PMID: 20838596]
  3. PHR1 plays an important role in sulfate inter-organ transport.
    [PMID: 21261953]
  4. A variant of the PHR1 binding site is highly enriched in the Arabidopsis phosphate-responsive phospholipase DZ2 coexpression network.
    [PMID: 22836502]
  5. that both PHR1 and PHL1 are major factors involved in the regulation of iron homeostasis
    [PMID: 23788639]
  6. PHR1 and PHO1 participate in the coregulation of Zn and Pi homeostasis.
    [PMID: 24420568]
  7. PHR1 is a key factor for metabolic reprogramming during phosphorus (P) limitation. The effects of pho2 or microRNA399 overexpression were comparatively minor.
    [PMID: 24894834]
  8. The relative strength of the SPX1/PHR1 interaction is thus directly influenced by phosphate (Pi), providing a link between Pi perception and signaling.
    [PMID: 25271326]
  9. PHL2 and PHR1 act redundantly as the key components of the central regulatory system controlling transcriptional responses to phosphate starvation.
    [PMID: 26586833]
  10. AtPHR1, a key transcription factor in Pi homeostasis of plants, was required for the negative regulation function of the AtMyb4 element in shoots. Additionally, the AtSPX3 promoter had a length limitation for activating gene expression.
    [PMID: 27382128]
  11. The results reveal a previously unknown link between Pro metabolism and phosphate nutrition and show that Pro biosynthesis is target of cross talk between Abscisic Acid (ABA) signaling and regulation of phosphate homeostasis through PHR1- and PHL1-mediated transcriptional activation of the P5CS1 gene.
    [PMID: 28765275]
  12. light and ethylene coordinately regulate PHR1 expression and Phosphate starvation responses through signaling convergence at the PHR1 promoter.
    [PMID: 28842534]
  13. These data suggest that, in the Pi-restored condition, AtSPX1 can bind to monomeric AtPHR1 in solution and therefore regulate PSI gene expression by tuning the AtPHR1-DNA-binding equilibrium.
    [PMID: 28887383]
  14. Transcription factors AUXIN RESPONSE FACTOR7 (ARF7) and ARF19 mutants showed down-regulated expression of PHOSPHATE STARVATION RESPONSE1 (PHR1) and downstream Pi starvation-induced genes in roots.
    [PMID: 30026290]
Cis-element ? help Back to Top
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Only moderately up-regulated by Pi starvation. {ECO:0000269|PubMed:11511543}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT2G02990(A), AT2G33770(R), AT2G45130(A), AT3G09922(A), AT3G23430(A), AT3G52190(A), AT5G20150(R), AT5G24770(A)
Phenotype -- Disruption Phenotype ? help Back to Top
Source Description
UniProtDISRUPTION PHENOTYPE: Strongly reduced shoot growth, and slightly increased root growth. Reduced expression of phosphate starvation-induced (PSI) genes, decreased cellular inorganic phosphate (Pi) content and shoot-to-root ratio, and impaired anthocyanin accumulation (PubMed:17927693). {ECO:0000269|PubMed:17927693}.
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT4G28610
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAJ3107990.0AJ310799.1 Arabidopsis thaliana mRNA for phosphate starvation response regulator 1 (phr1 gene).
GenBankJN0098020.0JN009802.1 UNVERIFIED: Lupinus polyphyllus phosphate starvation response regulator-like mRNA, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_194590.20.0phosphate starvation response 1
STRINGAT4G28610.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP7817262
Publications ? help Back to Top
  1. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
  2. Rubio V, et al.
    A conserved MYB transcription factor involved in phosphate starvation signaling both in vascular plants and in unicellular algae.
    Genes Dev., 2001. 15(16): p. 2122-33
  3. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
  4. Franco-Zorrilla JM, et al.
    The transcriptional control of plant responses to phosphate limitation.
    J. Exp. Bot., 2004. 55(396): p. 285-93
  5. Miura K, et al.
    The Arabidopsis SUMO E3 ligase SIZ1 controls phosphate deficiency responses.
    Proc. Natl. Acad. Sci. U.S.A., 2005. 102(21): p. 7760-5
  6. Liu Y, et al.
    Arabidopsis vegetative storage protein is an anti-insect acid phosphatase.
    Plant Physiol., 2005. 139(3): p. 1545-56
  7. Duarte JM, et al.
    Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis.
    Mol. Biol. Evol., 2006. 23(2): p. 469-78
  8. Gonz
    PHOSPHATE TRANSPORTER TRAFFIC FACILITATOR1 is a plant-specific SEC12-related protein that enables the endoplasmic reticulum exit of a high-affinity phosphate transporter in Arabidopsis.
    Plant Cell, 2005. 17(12): p. 3500-12
  9. Bari R,Datt Pant B,Stitt M,Scheible WR
    PHO2, microRNA399, and PHR1 define a phosphate-signaling pathway in plants.
    Plant Physiol., 2006. 141(3): p. 988-99
  10. K
    Tissue-specific expression of tomato Ribonuclease LX during phosphate starvation-induced root growth.
    J. Exp. Bot., 2006. 57(14): p. 3717-26
  11. M
    Genome-wide analysis of the Arabidopsis leaf transcriptome reveals interaction of phosphate and sugar metabolism.
    Plant Physiol., 2007. 143(1): p. 156-71
  12. Stefanovic A, et al.
    Members of the PHO1 gene family show limited functional redundancy in phosphate transfer to the shoot, and are regulated by phosphate deficiency via distinct pathways.
    Plant J., 2007. 50(6): p. 982-94
  13. Franco-Zorrilla JM, et al.
    Target mimicry provides a new mechanism for regulation of microRNA activity.
    Nat. Genet., 2007. 39(8): p. 1033-7
  14. Nilsson L,M
    Increased expression of the MYB-related transcription factor, PHR1, leads to enhanced phosphate uptake in Arabidopsis thaliana.
    Plant Cell Environ., 2007. 30(12): p. 1499-512
  15. Ribot C,Wang Y,Poirier Y
    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.
    Planta, 2008. 227(5): p. 1025-36
  16. Zhou J, et al.
    OsPHR2 is involved in phosphate-starvation signaling and excessive phosphate accumulation in shoots of plants.
    Plant Physiol., 2008. 146(4): p. 1673-86
  17. Duan K, et al.
    Characterization of a sub-family of Arabidopsis genes with the SPX domain reveals their diverse functions in plant tolerance to phosphorus starvation.
    Plant J., 2008. 54(6): p. 965-75
  18. Gaude N,Nakamura Y,Scheible WR,Ohta H,D
    Phospholipase C5 (NPC5) is involved in galactolipid accumulation during phosphate limitation in leaves of Arabidopsis.
    Plant J., 2008. 56(1): p. 28-39
  19. Vald
    Essential role of MYB transcription factor: PvPHR1 and microRNA: PvmiR399 in phosphorus-deficiency signalling in common bean roots.
    Plant Cell Environ., 2008. 31(12): p. 1834-43
  20. Grennan AK
    Phosphate accumulation in plants: signaling.
    Plant Physiol., 2008. 148(1): p. 3-5
  21. Wang Y, et al.
    Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis.
    Plant Physiol., 2008. 148(3): p. 1201-11
  22. Vald
    Transcriptional regulation and signaling in phosphorus starvation: what about legumes?
    J Integr Plant Biol, 2008. 50(10): p. 1213-22
  23. Jones AM, et al.
    Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis thaliana.
    J Proteomics, 2009. 72(3): p. 439-51
  24. Reiland S, et al.
    Large-scale Arabidopsis phosphoproteome profiling reveals novel chloroplast kinase substrates and phosphorylation networks.
    Plant Physiol., 2009. 150(2): p. 889-903
  25. Wu P,Wang X
    Role of OsPHR2 on phosphorus homeostasis and root hairs development in rice (Oryza sativa L.).
    Plant Signal Behav, 2008. 3(9): p. 674-5
  26. Lundmark M,K
    Global analysis of microRNA in Arabidopsis in response to phosphate starvation as studied by locked nucleic acid-based microarrays.
    Physiol Plant, 2010. 140(1): p. 57-68
  27. Castells E, et al.
    det1-1-induced UV-C hyposensitivity through UVR3 and PHR1 photolyase gene over-expression.
    Plant J., 2010. 63(3): p. 392-404
  28. Bustos R, et al.
    A central regulatory system largely controls transcriptional activation and repression responses to phosphate starvation in Arabidopsis.
    PLoS Genet., 2010. 6(9): p. e1001102
  29. Thibaud MC, et al.
    Dissection of local and systemic transcriptional responses to phosphate starvation in Arabidopsis.
    Plant J., 2010. 64(5): p. 775-89
  30. Rouached H,Secco D,Arpat B,Poirier Y
    The transcription factor PHR1 plays a key role in the regulation of sulfate shoot-to-root flux upon phosphate starvation in Arabidopsis.
    BMC Plant Biol., 2011. 11: p. 19
  31. Li G, et al.
    Coordinated transcriptional regulation underlying the circadian clock in Arabidopsis.
    Nat. Cell Biol., 2011. 13(5): p. 616-22
  32. Castrillo G, et al.
    Speeding cis-trans regulation discovery by phylogenomic analyses coupled with screenings of an arrayed library of Arabidopsis transcription factors.
    PLoS ONE, 2011. 6(6): p. e21524
  33. Nilsson L,Lundmark M,Jensen PE,Nielsen TH
    The Arabidopsis transcription factor PHR1 is essential for adaptation to high light and retaining functional photosynthesis during phosphate starvation.
    Physiol Plant, 2012. 144(1): p. 35-47
  34. Oropeza-Aburto A, et al.
    Functional analysis of the Arabidopsis PLDZ2 promoter reveals an evolutionarily conserved low-Pi-responsive transcriptional enhancer element.
    J. Exp. Bot., 2012. 63(5): p. 2189-202
  35. Acevedo-Hern
    A specific variant of the PHR1 binding site is highly enriched in the Arabidopsis phosphate-responsive phospholipase DZ2 coexpression network.
    Plant Signal Behav, 2012. 7(8): p. 914-7
  36. Jain A,Nagarajan VK,Raghothama KG
    Transcriptional regulation of phosphate acquisition by higher plants.
    Cell. Mol. Life Sci., 2012. 69(19): p. 3207-24
  37. Wang J, et al.
    A phosphate starvation response regulator Ta-PHR1 is involved in phosphate signalling and increases grain yield in wheat.
    Ann. Bot., 2013. 111(6): p. 1139-53
  38. Bournier M, et al.
    Arabidopsis ferritin 1 (AtFer1) gene regulation by the phosphate starvation response 1 (AtPHR1) transcription factor reveals a direct molecular link between iron and phosphate homeostasis.
    J. Biol. Chem., 2013. 288(31): p. 22670-80
  39. Matsui K,Togami J,Mason JG,Chandler SF,Tanaka Y
    Enhancement of phosphate absorption by garden plants by genetic engineering: a new tool for phytoremediation.
    Biomed Res Int, 2013. 2013: p. 182032
  40. Khan GA, et al.
    Coordination between zinc and phosphate homeostasis involves the transcription factor PHR1, the phosphate exporter PHO1, and its homologue PHO1;H3 in Arabidopsis.
    J. Exp. Bot., 2014. 65(3): p. 871-84
  41. Klecker M, et al.
    A Shoot-Specific Hypoxic Response of Arabidopsis Sheds Light on the Role of the Phosphate-Responsive Transcription Factor PHOSPHATE STARVATION RESPONSE1.
    Plant Physiol., 2014. 165(2): p. 774-790
  42. Pant BD, et al.
    Identification of primary and secondary metabolites with phosphorus status-dependent abundance in Arabidopsis, and of the transcription factor PHR1 as a major regulator of metabolic changes during phosphorus limitation.
    Plant Cell Environ., 2015. 38(1): p. 172-87
  43. Puga MI, et al.
    SPX1 is a phosphate-dependent inhibitor of Phosphate Starvation Response 1 in Arabidopsis.
    Proc. Natl. Acad. Sci. U.S.A., 2014. 111(41): p. 14947-52
  44. Pant BD, et al.
    The transcription factor PHR1 regulates lipid remodeling and triacylglycerol accumulation in Arabidopsis thaliana during phosphorus starvation.
    J. Exp. Bot., 2015. 66(7): p. 1907-18
  45. Jost R, et al.
    Differentiating phosphate-dependent and phosphate-independent systemic phosphate-starvation response networks in Arabidopsis thaliana through the application of phosphite.
    J. Exp. Bot., 2015. 66(9): p. 2501-14
  46. Jin J, et al.
    An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors.
    Mol. Biol. Evol., 2015. 32(7): p. 1767-73
  47. Zhou Z, et al.
    SPX proteins regulate Pi homeostasis and signaling in different subcellular level.
    Plant Signal Behav, 2015. 10(9): p. e1061163
  48. Bonnot C, et al.
    A chemical genetic strategy identify the PHOSTIN, a synthetic molecule that triggers phosphate starvation responses in Arabidopsis thaliana.
    New Phytol., 2016. 209(1): p. 161-76
  49. Sun L,Song L,Zhang Y,Zheng Z,Liu D
    Arabidopsis PHL2 and PHR1 Act Redundantly as the Key Components of the Central Regulatory System Controlling Transcriptional Responses to Phosphate Starvation.
    Plant Physiol., 2016. 170(1): p. 499-514
  50. Khan GA,Vogiatzaki E,Glauser G,Poirier Y
    Phosphate Deficiency Induces the Jasmonate Pathway and Enhances Resistance to Insect Herbivory.
    Plant Physiol., 2016. 171(1): p. 632-44
  51. Velasco VM, et al.
    Acclimation of the crucifer Eutrema salsugineum to phosphate limitation is associated with constitutively high expression of phosphate-starvation genes.
    Plant Cell Environ., 2016. 39(8): p. 1818-34
  52. Yong-Villalobos L, et al.
    Phosphate starvation induces DNA methylation in the vicinity of cis-acting elements known to regulate the expression of phosphate-responsive genes.
    Plant Signal Behav, 2016. 11(5): p. e1173300
  53. Li Y,Wu H,Fan H,Zhao T,Ling HQ
    Characterization of the AtSPX3 Promoter Elucidates its Complex Regulation in Response to Phosphorus Deficiency.
    Plant Cell Physiol., 2016. 57(8): p. 1767-78
  54. Zhang H,Huang L,Hong Y,Song F
    BOTRYTIS-INDUCED KINASE1, a plasma membrane-localized receptor-like protein kinase, is a negative regulator of phosphate homeostasis in Arabidopsis thaliana.
    BMC Plant Biol., 2016. 16(1): p. 152
  55. Yuan J, et al.
    Systematic characterization of novel lncRNAs responding to phosphate starvation in Arabidopsis thaliana.
    BMC Genomics, 2016. 17: p. 655
  56. Linn J, et al.
    Root Cell-Specific Regulators of Phosphate-Dependent Growth.
    Plant Physiol., 2017. 174(3): p. 1969-1989
  57. Aleksza D,Horváth GV,Sándor G,Szabados L
    Proline Accumulation Is Regulated by Transcription Factors Associated with Phosphate Starvation.
    Plant Physiol., 2017. 175(1): p. 555-567
  58. Liu Y, et al.
    Light and Ethylene Coordinately Regulate the Phosphate Starvation Response through Transcriptional Regulation of PHOSPHATE STARVATION RESPONSE1.
    Plant Cell, 2017. 29(9): p. 2269-2284
  59. Qi W,Manfield IW,Muench SP,Baker A
    AtSPX1 affects the AtPHR1-DNA-binding equilibrium by binding monomeric AtPHR1 in solution.
    Biochem. J., 2017. 474(21): p. 3675-3687
  60. Huang KL, et al.
    The ARF7 and ARF19 Transcription Factors Positively Regulate PHOSPHATE STARVATION RESPONSE1 in Arabidopsis Roots.
    Plant Physiol., 2018. 178(1): p. 413-427
  61. Jiang M, et al.
    Structural basis for the Target DNA recognition and binding by the MYB domain of phosphate starvation response 1.
    FEBS J., 2019.