PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT3G59060.1
Common NameBHLH65, EN103, F17J16.110, PIF5, PIL6
Organism
Arabidopsis thaliana
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 bHLH
Protein Properties Length: 442aa    MW: 49042.7 Da    PI: 6.2418
Description phytochrome interacting factor 3-like 6
Gene Model
Gene Model ID Type Source Coding Sequence
AT3G59060.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1HLH55.11.3e-17260306455
                  HHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS
          HLH   4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                   hn  ErrRRdriN+++  L+el+P++      + +Ka+iL +A++Y+ksLq
  AT3G59060.1 260 VHNLSERRRRDRINERMKALQELIPHC-----SRTDKASILDEAIDYLKSLQ 306
                  6*************************9.....79*****************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:4.10.280.102.9E-21254314IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamilySSF474599.55E-21254315IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profilePS5088818.94256305IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
CDDcd000831.87E-10259310No hitNo description
PfamPF000106.3E-15260306IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003536.1E-18262311IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009585Biological Processred, far-red light phototransduction
GO:0009693Biological Processethylene biosynthetic process
GO:0010244Biological Processresponse to low fluence blue light stimulus by blue low-fluence system
GO:0010600Biological Processregulation of auxin biosynthetic process
GO:0010928Biological Processregulation of auxin mediated signaling pathway
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0005515Molecular Functionprotein binding
GO:0046983Molecular Functionprotein dimerization activity
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0008019anatomyleaf lamina base
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009025anatomyvascular leaf
PO:0009029anatomystamen
PO:0009030anatomycarpel
PO:0009031anatomysepal
PO:0009032anatomypetal
PO:0009046anatomyflower
PO:0009047anatomystem
PO:0020030anatomycotyledon
PO:0020038anatomypetiole
PO:0020100anatomyhypocotyl
PO:0020137anatomyleaf apex
PO:0025022anatomycollective leaf structure
PO:0001054developmental stagevascular leaf senescent 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: 442 aa     Download sequence    Send to blast
MEQVFADWNF EDNFHMSTNK RSIRPEDELV ELLWRDGQVV LQSQARREPS VQVQTHKQET  60
LRKPNNIFLD NQETVQKPNY AALDDQETVS WIQYPPDDVI DPFESEFSSH FFSSIDHLGG  120
PEKPRTIEET VKHEAQAMAP PKFRSSVITV GPSHCGSNQS TNIHQATTLP VSMSDRSKNV  180
EERLDTSSGG SSGCSYGRNN KETVSGTSVT IDRKRKHVMD ADQESVSQSD IGLTSTDDQT  240
MGNKSSQRSG STRRSRAAEV HNLSERRRRD RINERMKALQ ELIPHCSRTD KASILDEAID  300
YLKSLQMQLQ VMWMGSGMAA AAAAAASPMM FPGVQSSPYI NQMAMQSQMQ LSQFPVMNRS  360
APQNHPGLVC QNPVQLQLQA QNQILSEQLA RYMGGIPQMP PAGNQTVQQQ PADMLGFGSP  420
AGPQSQLSAP ATTDSLHMGK IG
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1264269ERRRRD
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.434370.0leaf| vegetative tissue
Expression -- Microarray ? help Back to Top
Source ID E-value
Genevisible251497_at0.0
Expression AtlasAT3G59060-
AtGenExpressAT3G59060-
ATTED-IIAT3G59060-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Circadian-controlled expression. {ECO:0000269|PubMed:15356333}.
UniprotTISSUE SPECIFICITY: Expressed in roots, leaves, stems, and flowers. {ECO:0000269|PubMed:12679534}.
Functional Description ? help Back to Top
Source Description
TAIREncodes a novel Myc-related bHLH transcription factor, which physically associated with APRR1/TOC1 and is a member of PIF3 transcription factor family. Involved in shade avoidance. Functions as negative regulator of PhyB. Protein levels are modulated by phytochrome B.
UniProtTranscription factor acting negatively in the phytochrome B signaling pathway to promote the shade-avoidance response. Regulates PHYB abundance at the post-transcriptional level, possibly via the ubiquitin-proteasome pathway. Promotes ethylene activity in the dark. May regulate the expression of a subset of genes by binding to the G-box motif. Might be involved in the integration of light-signals to control both circadian and photomorphogenic processes. Activated by CRY1 and CRY2 in response to low blue light (LBL) by direct binding at chromatin on E-box variant 5'-CA[CT]GTG-3' to stimulate specific gene expression to adapt global physiology (e.g. hypocotyl elongation in low blue light) (PubMed:26724867). {ECO:0000269|PubMed:12826627, ECO:0000269|PubMed:15356333, ECO:0000269|PubMed:15486100, ECO:0000269|PubMed:17589502, ECO:0000269|PubMed:18047474, ECO:0000269|PubMed:18065691, ECO:0000269|PubMed:26724867}.
Function -- GeneRIF ? help Back to Top
  1. Photobiological and genetic evidence indicated that the photoactivated phytochrome molecule acts to induce PIF5 phosphorylation, phyA and phyB redundantly dominate this process.
    [PMID: 17827270]
  2. findings show that PIF4 and PIF5 act early in the phytochrome signaling pathways to promote the shade-avoidance response
    [PMID: 18047474]
  3. Data indicate that overexpressed PIF5 causes altered ethylene levels, which promote the triple response in darkness, whereas in the light, the interaction of photoactivated phyB with PIF5 causes degradation of the photoreceptor protein.
    [PMID: 18065691]
  4. Phytochrome interacting factors 4 and 5 are part of an inhibitory mechanism that represses the expression of some light-responsive genes in the dark and they are needed for full expression of several growth-related genes in the light. [PIF5]
    [PMID: 19619162]
  5. PIF4 and PIF5 responsible not only for red light signaling through the phytochromes but also for blue light signaling in the photomorphogenic control of hypocotyl elongation
    [PMID: 21150090]
  6. Studies indicate that phytochromes inhibit hypocotyl negative gravitropism by inhibiting four phytochrome-interacting factors (PIF1, PIF3, PIF4, PIF5), as shown by hypocotyl agravitropism of dark-grown pif1 pif3 pif4 pif5 quadruple mutants.
    [PMID: 21220341]
  7. At least two downstream modules participate in diurnal rhythmic hypocotyl growth: PIF4 and/or PIF5 modulation of auxin-related pathways and PIF-independent regulation of the gibberellic acid (GA) pathway.
    [PMID: 21430186]
  8. an external coincidence model involving the clock-controlled PIF4/PIF5-ATHB2 pathway is crucial for the diurnal and photoperiodic control of plant growth in A. thaliana.
    [PMID: 21666227]
  9. PhyB-mediated, post-translational regulation allows PIF3 accumulation to peak just before dawn, at which time it accelerates hypocotyl growth, together with PIF4 and PIF5, by directly regulating the induction of growth-related genes.
    [PMID: 22409654]
  10. regulates elongation growth by controlling directly the expression of genes that code for auxin biosynthesis and auxin signaling components
    [PMID: 22536829]
  11. The ability of Glc to induce IAA biosynthesis was upregulated in the pif1 pif3 pif4 pif5 quadruple mutant line compared with the wild type.
    [PMID: 23209113]
  12. Data indicate that PIF4 and PIF5 negatively regulate auxin signaling. that PIF4 and PIF5 negatively modulate auxin-mediated phototropism through directly activating IAA19 and IAA29, which physically interact with auxin factor7 (ARF7).
    [PMID: 23757399]
  13. circadian clock and PIF4/PIF5 mediated external coincidence mechanism in transcription of ST2A
    [PMID: 24317064]
  14. PIF1, PIF3, PIF4, and PIF5 act together to promote and optimize growth under photoperiodic conditions.
    [PMID: 24420574]
  15. The PIF4 and PIF5 transcription factors promote flowering by at least two means: inducing FT expression in warm night and acting outside of FT by an unknown mechanism in warm days.
    [PMID: 24574484]
  16. Phytochrome-interacting transcription factors PIF4 and PIF5 induce leaf senescence in Arabidopsis.
    [PMID: 25119965]
  17. The expression level of PIF3, 4, and 5 was significantly up-regulated during both age-triggered and dark-induced leaf senescence.
    [PMID: 25296857]
  18. PIF5 is a key factor that positively regulates dark-induced senescence upstream of ORE1 and regulates chlorophyll breakdown upstream of SGR and NYC1.
    [PMID: 26089152]
  19. PIF4 and PIF5 negatively regulate red light-induced anthocyanin accumulation through transcriptional repression of the anthocyanin biosynthetic genes in Arabidopsis.
    [PMID: 26259175]
  20. outline a novel phytochrome signaling mechanism by which TOPP4-mediated dephosphorylation of PIF5 attenuates phytochrome-dependent light responses
    [PMID: 26704640]
  21. For growth under a canopy, where blue light is diminished, CRY1 and CRY2 perceive this change and respond by directly contacting two bHLH transcription factors, PIF4 and PIF5.
    [PMID: 26724867]
  22. COP1 promotes the degradation of HFR1 under shade, thus increasing the ability of PIFs to control gene expression, increase auxin levels and promote stem growth.
    [PMID: 27105120]
  23. COG1 binds to the promoter regions of PIF4 and PIF5, and PIF4 and PIF5 bind to the promoter regions of key Brassinosteroid biosynthetic genes, such as DWF4 and BR6ox2, to directly promote their expression.
    [PMID: 28438793]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00082ChIP-seq26531826Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT3G59060.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Follow a free-running robust circadian rhythm, with higher levels during the light phase. Rapidly induced by light in etiolated plants. Up-regulated by white light. Rapid degradation after red light exposure (at protein level). Accumulates to high levels in the dark, is selectively degraded in response to red light and remains at high levels under shade-mimicking conditions. {ECO:0000269|PubMed:12826627, ECO:0000269|PubMed:17589502, ECO:0000269|PubMed:18047474}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source Upstream Regulator (A: Activate/R: Repress)
ATRM AT2G46830 (A)
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT2G22810(A), AT4G37770(A), AT5G35840(R)
Regulation -- Hormone ? help Back to Top
Source Hormone
AHDethylene
Interaction ? help Back to Top
Source Intact With
BioGRIDAT1G09530, AT1G02340
IntActSearch Q84LH8
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT3G59060
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK3173740.0AK317374.1 Arabidopsis thaliana AT3G59060 mRNA, complete cds, clone: RAFL25-22-H20.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_851021.10.0phytochrome interacting factor 3-like 6
SwissprotQ84LH80.0PIF5_ARATH; Transcription factor PIF5
TrEMBLB9DH290.0B9DH29_ARATH; AT3G59060 protein
STRINGAT3G59060.40.0(Arabidopsis thaliana)
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
    [PMID:11118137]
  2. Ma L, et al.
    Genomic evidence for COP1 as a repressor of light-regulated gene expression and development in Arabidopsis.
    Plant Cell, 2002. 14(10): p. 2383-98
    [PMID:12368493]
  3. Heim MA, et al.
    The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity.
    Mol. Biol. Evol., 2003. 20(5): p. 735-47
    [PMID:12679534]
  4. Yamashino T, et al.
    A Link between circadian-controlled bHLH factors and the APRR1/TOC1 quintet in Arabidopsis thaliana.
    Plant Cell Physiol., 2003. 44(6): p. 619-29
    [PMID:12826627]
  5. Toledo-Ortiz G,Huq E,Quail PH
    The Arabidopsis basic/helix-loop-helix transcription factor family.
    Plant Cell, 2003. 15(8): p. 1749-70
    [PMID:12897250]
  6. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
    [PMID:14593172]
  7. Ito S, et al.
    Characterization of the APRR9 pseudo-response regulator belonging to the APRR1/TOC1 quintet in Arabidopsis thaliana.
    Plant Cell Physiol., 2003. 44(11): p. 1237-45
    [PMID:14634162]
  8. Fujimori T,Yamashino T,Kato T,Mizuno T
    Circadian-controlled basic/helix-loop-helix factor, PIL6, implicated in light-signal transduction in Arabidopsis thaliana.
    Plant Cell Physiol., 2004. 45(8): p. 1078-86
    [PMID:15356333]
  9. Khanna R, et al.
    A novel molecular recognition motif necessary for targeting photoactivated phytochrome signaling to specific basic helix-loop-helix transcription factors.
    Plant Cell, 2004. 16(11): p. 3033-44
    [PMID:15486100]
  10. Ito S, et al.
    Genetic linkages between circadian clock-associated components and phytochrome-dependent red light signal transduction in Arabidopsis thaliana.
    Plant Cell Physiol., 2007. 48(7): p. 971-83
    [PMID:17519251]
  11. Nozue K, et al.
    Rhythmic growth explained by coincidence between internal and external cues.
    Nature, 2007. 448(7151): p. 358-61
    [PMID:17589502]
  12. Shen Y,Khanna R,Carle CM,Quail PH
    Phytochrome induces rapid PIF5 phosphorylation and degradation in response to red-light activation.
    Plant Physiol., 2007. 145(3): p. 1043-51
    [PMID:17827270]
  13. Lorrain S,Allen T,Duek PD,Whitelam GC,Fankhauser C
    Phytochrome-mediated inhibition of shade avoidance involves degradation of growth-promoting bHLH transcription factors.
    Plant J., 2008. 53(2): p. 312-23
    [PMID:18047474]
  14. Khanna R, et al.
    The basic helix-loop-helix transcription factor PIF5 acts on ethylene biosynthesis and phytochrome signaling by distinct mechanisms.
    Plant Cell, 2007. 19(12): p. 3915-29
    [PMID:18065691]
  15. Kumagai T, et al.
    The common function of a novel subfamily of B-Box zinc finger proteins with reference to circadian-associated events in Arabidopsis thaliana.
    Biosci. Biotechnol. Biochem., 2008. 72(6): p. 1539-49
    [PMID:18540109]
  16. Leivar P, et al.
    Multiple phytochrome-interacting bHLH transcription factors repress premature seedling photomorphogenesis in darkness.
    Curr. Biol., 2008. 18(23): p. 1815-23
    [PMID:19062289]
  17. Niwa Y,Yamashino T,Mizuno T
    The circadian clock regulates the photoperiodic response of hypocotyl elongation through a coincidence mechanism in Arabidopsis thaliana.
    Plant Cell Physiol., 2009. 50(4): p. 838-54
    [PMID:19233867]
  18. Shin J, et al.
    Phytochromes promote seedling light responses by inhibiting four negatively-acting phytochrome-interacting factors.
    Proc. Natl. Acad. Sci. U.S.A., 2009. 106(18): p. 7660-5
    [PMID:19380720]
  19. Jaspers P, et al.
    Unequally redundant RCD1 and SRO1 mediate stress and developmental responses and interact with transcription factors.
    Plant J., 2009. 60(2): p. 268-79
    [PMID:19548978]
  20. Lorrain S,Trevisan M,Pradervand S,Fankhauser C
    Phytochrome interacting factors 4 and 5 redundantly limit seedling de-etiolation in continuous far-red light.
    Plant J., 2009. 60(3): p. 449-61
    [PMID:19619162]
  21. Rawat R, et al.
    REVEILLE1, a Myb-like transcription factor, integrates the circadian clock and auxin pathways.
    Proc. Natl. Acad. Sci. U.S.A., 2009. 106(39): p. 16883-8
    [PMID:19805390]
  22. Hornitschek P,Lorrain S,Zoete V,Michielin O,Fankhauser C
    Inhibition of the shade avoidance response by formation of non-DNA binding bHLH heterodimers.
    EMBO J., 2009. 28(24): p. 3893-902
    [PMID:19851283]
  23. Leivar P, et al.
    Definition of early transcriptional circuitry involved in light-induced reversal of PIF-imposed repression of photomorphogenesis in young Arabidopsis seedlings.
    Plant Cell, 2009. 21(11): p. 3535-53
    [PMID:19920208]
  24. Skinner MK,Rawls A,Wilson-Rawls J,Roalson EH
    Basic helix-loop-helix transcription factor gene family phylogenetics and nomenclature.
    Differentiation, 2010. 80(1): p. 1-8
    [PMID:20219281]
  25. Jang IC,Henriques R,Seo HS,Nagatani A,Chua NH
    Arabidopsis PHYTOCHROME INTERACTING FACTOR proteins promote phytochrome B polyubiquitination by COP1 E3 ligase in the nucleus.
    Plant Cell, 2010. 22(7): p. 2370-83
    [PMID:20605855]
  26. Hanada K, et al.
    Functional compensation of primary and secondary metabolites by duplicate genes in Arabidopsis thaliana.
    Mol. Biol. Evol., 2011. 28(1): p. 377-82
    [PMID:20736450]
  27. Richter R,Behringer C,M
    The GATA-type transcription factors GNC and GNL/CGA1 repress gibberellin signaling downstream from DELLA proteins and PHYTOCHROME-INTERACTING FACTORS.
    Genes Dev., 2010. 24(18): p. 2093-104
    [PMID:20844019]
  28. Kunihiro A,Yamashino T,Mizuno T
    PHYTOCHROME-INTERACTING FACTORS PIF4 and PIF5 are implicated in the regulation of hypocotyl elongation in response to blue light in Arabidopsis thaliana.
    Biosci. Biotechnol. Biochem., 2010. 74(12): p. 2538-41
    [PMID:21150090]
  29. Kim K, et al.
    Phytochromes inhibit hypocotyl negative gravitropism by regulating the development of endodermal amyloplasts through phytochrome-interacting factors.
    Proc. Natl. Acad. Sci. U.S.A., 2011. 108(4): p. 1729-34
    [PMID:21220341]
  30. Nozue K,Harmer SL,Maloof JN
    Genomic analysis of circadian clock-, light-, and growth-correlated genes reveals PHYTOCHROME-INTERACTING FACTOR5 as a modulator of auxin signaling in Arabidopsis.
    Plant Physiol., 2011. 156(1): p. 357-72
    [PMID:21430186]
  31. Stewart JL,Maloof JN,Nemhauser JL
    PIF genes mediate the effect of sucrose on seedling growth dynamics.
    PLoS ONE, 2011. 6(5): p. e19894
    [PMID:21625438]
  32. Kunihiro A, et al.
    Phytochrome-interacting factor 4 and 5 (PIF4 and PIF5) activate the homeobox ATHB2 and auxin-inducible IAA29 genes in the coincidence mechanism underlying photoperiodic control of plant growth of Arabidopsis thaliana.
    Plant Cell Physiol., 2011. 52(8): p. 1315-29
    [PMID:21666227]
  33. Nusinow DA, et al.
    The ELF4-ELF3-LUX complex links the circadian clock to diurnal control of hypocotyl growth.
    Nature, 2011. 475(7356): p. 398-402
    [PMID:21753751]
  34. Bu Q,Castillon A,Chen F,Zhu L,Huq E
    Dimerization and blue light regulation of PIF1 interacting bHLH proteins in Arabidopsis.
    Plant Mol. Biol., 2011. 77(4-5): p. 501-11
    [PMID:21928113]
  35. Franklin KA, et al.
    Phytochrome-interacting factor 4 (PIF4) regulates auxin biosynthesis at high temperature.
    Proc. Natl. Acad. Sci. U.S.A., 2011. 108(50): p. 20231-5
    [PMID:22123947]
  36. Chow BY,Helfer A,Nusinow DA,Kay SA
    ELF3 recruitment to the PRR9 promoter requires other Evening Complex members in the Arabidopsis circadian clock.
    Plant Signal Behav, 2012. 7(2): p. 170-3
    [PMID:22307044]
  37. Sellaro R,Pac
    Diurnal dependence of growth responses to shade in Arabidopsis: role of hormone, clock, and light signaling.
    Mol Plant, 2012. 5(3): p. 619-28
    [PMID:22311777]
  38. Soy J, et al.
    Phytochrome-imposed oscillations in PIF3 protein abundance regulate hypocotyl growth under diurnal light/dark conditions in Arabidopsis.
    Plant J., 2012. 71(3): p. 390-401
    [PMID:22409654]
  39. Leivar P,Monte E,Cohn MM,Quail PH
    Phytochrome signaling in green Arabidopsis seedlings: impact assessment of a mutually negative phyB-PIF feedback loop.
    Mol Plant, 2012. 5(3): p. 734-49
    [PMID:22492120]
  40. Hornitschek P, et al.
    Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling.
    Plant J., 2012. 71(5): p. 699-711
    [PMID:22536829]
  41. Casal JJ
    Shade avoidance.
    Arabidopsis Book, 2012. 10: p. e0157
    [PMID:22582029]
  42. Shin J,Heidrich K,Sanchez-Villarreal A,Parker JE,Davis SJ
    TIME FOR COFFEE represses accumulation of the MYC2 transcription factor to provide time-of-day regulation of jasmonate signaling in Arabidopsis.
    Plant Cell, 2012. 24(6): p. 2470-82
    [PMID:22693280]
  43. Reymond MC, et al.
    A light-regulated genetic module was recruited to carpel development in Arabidopsis following a structural change to SPATULA.
    Plant Cell, 2012. 24(7): p. 2812-25
    [PMID:22851763]
  44. Trivellini A, et al.
    Carbon deprivation-driven transcriptome reprogramming in detached developmentally arresting Arabidopsis inflorescences.
    Plant Physiol., 2012. 160(3): p. 1357-72
    [PMID:22930749]
  45. Lilley JL,Gee CW,Sairanen I,Ljung K,Nemhauser JL
    An endogenous carbon-sensing pathway triggers increased auxin flux and hypocotyl elongation.
    Plant Physiol., 2012. 160(4): p. 2261-70
    [PMID:23073695]
  46. Sairanen I, et al.
    Soluble carbohydrates regulate auxin biosynthesis via PIF proteins in Arabidopsis.
    Plant Cell, 2012. 24(12): p. 4907-16
    [PMID:23209113]
  47. Takase M,Mizoguchi T,Kozuka T,Tsukaya H
    The unique function of the Arabidopsis circadian clock gene PRR5 in the regulation of shade avoidance response.
    Plant Signal Behav, 2013. 8(4): p. e23534
    [PMID:23333981]
  48. Sun J,Qi L,Li Y,Zhai Q,Li C
    PIF4 and PIF5 transcription factors link blue light and auxin to regulate the phototropic response in Arabidopsis.
    Plant Cell, 2013. 25(6): p. 2102-14
    [PMID:23757399]
  49. Carabelli M,Turchi L,Ruzza V,Morelli G,Ruberti I
    Homeodomain-Leucine Zipper II family of transcription factors to the limelight: central regulators of plant development.
    Plant Signal Behav, 2014.
    [PMID:23838958]
  50. Karayekov E,Sellaro R,Legris M,Yanovsky MJ,Casal JJ
    Heat shock-induced fluctuations in clock and light signaling enhance phytochrome B-mediated Arabidopsis deetiolation.
    Plant Cell, 2013. 25(8): p. 2892-906
    [PMID:23933882]
  51. Yamashino T,Kitayama M,Mizuno T
    Transcription of ST2A encoding a sulfotransferase family protein that is involved in jasmonic acid metabolism is controlled according to the circadian clock- and PIF4/PIF5-mediated external coincidence mechanism in Arabidopsis thaliana.
    Biosci. Biotechnol. Biochem., 2013. 77(12): p. 2454-60
    [PMID:24317064]
  52. Mannen K, et al.
    Coordinated transcriptional regulation of isopentenyl diphosphate biosynthetic pathway enzymes in plastids by phytochrome-interacting factor 5.
    Biochem. Biophys. Res. Commun., 2014. 443(2): p. 768-74
    [PMID:24342623]
  53. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  54. Soy J,Leivar P,Monte E
    PIF1 promotes phytochrome-regulated growth under photoperiodic conditions in Arabidopsis together with PIF3, PIF4, and PIF5.
    J. Exp. Bot., 2014. 65(11): p. 2925-36
    [PMID:24420574]
  55. Li Y,Jing Y,Li J,Xu G,Lin R
    Arabidopsis VQ MOTIF-CONTAINING PROTEIN29 represses seedling deetiolation by interacting with PHYTOCHROME-INTERACTING FACTOR1.
    Plant Physiol., 2014. 164(4): p. 2068-80
    [PMID:24569844]
  56. Thines BC,Youn Y,Duarte MI,Harmon FG
    The time of day effects of warm temperature on flowering time involve PIF4 and PIF5.
    J. Exp. Bot., 2014. 65(4): p. 1141-51
    [PMID:24574484]
  57. Sakuraba Y, et al.
    Phytochrome-interacting transcription factors PIF4 and PIF5 induce leaf senescence in Arabidopsis.
    Nat Commun, 2014. 5: p. 4636
    [PMID:25119965]
  58. Dong J, et al.
    Arabidopsis DE-ETIOLATED1 represses photomorphogenesis by positively regulating phytochrome-interacting factors in the dark.
    Plant Cell, 2014. 26(9): p. 3630-45
    [PMID:25248553]
  59. Di C, et al.
    Characterization of stress-responsive lncRNAs in Arabidopsis thaliana by integrating expression, epigenetic and structural features.
    Plant J., 2014. 80(5): p. 848-61
    [PMID:25256571]
  60. Dornbusch T,Michaud O,Xenarios I,Fankhauser C
    Differentially phased leaf growth and movements in Arabidopsis depend on coordinated circadian and light regulation.
    Plant Cell, 2014. 26(10): p. 3911-21
    [PMID:25281688]
  61. Song Y, et al.
    Age-triggered and dark-induced leaf senescence require the bHLH transcription factors PIF3, 4, and 5.
    Mol Plant, 2014. 7(12): p. 1776-87
    [PMID:25296857]
  62. Seaton DD, et al.
    Linked circadian outputs control elongation growth and flowering in response to photoperiod and temperature.
    Mol. Syst. Biol., 2015. 11(1): p. 776
    [PMID:25600997]
  63. Filo J, et al.
    Gibberellin driven growth in elf3 mutants requires PIF4 and PIF5.
    Plant Signal Behav, 2015. 10(3): p. e992707
    [PMID:25738547]
  64. 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
    [PMID:25750178]
  65. Qiu Y, et al.
    HEMERA Couples the Proteolysis and Transcriptional Activity of PHYTOCHROME INTERACTING FACTORs in Arabidopsis Photomorphogenesis.
    Plant Cell, 2015. 27(5): p. 1409-27
    [PMID:25944101]
  66. Zhang Y,Liu Z,Chen Y,He JX,Bi Y
    PHYTOCHROME-INTERACTING FACTOR 5 (PIF5) positively regulates dark-induced senescence and chlorophyll degradation in Arabidopsis.
    Plant Sci., 2015. 237: p. 57-68
    [PMID:26089152]
  67. Mizuno T,Oka H,Yoshimura F,Ishida K,Yamashino T
    Insight into the mechanism of end-of-day far-red light (EODFR)-induced shade avoidance responses in Arabidopsis thaliana.
    Biosci. Biotechnol. Biochem., 2015. 79(12): p. 1987-94
    [PMID:26193333]
  68. Liu Z, et al.
    Phytochrome-interacting factors PIF4 and PIF5 negatively regulate anthocyanin biosynthesis under red light in Arabidopsis seedlings.
    Plant Sci., 2015. 238: p. 64-72
    [PMID:26259175]
  69. Galvão VC,Collani S,Horrer D,Schmid M
    Gibberellic acid signaling is required for ambient temperature-mediated induction of flowering in Arabidopsis thaliana.
    Plant J., 2015. 84(5): p. 949-62
    [PMID:26466761]
  70. Miyazaki Y, et al.
    Enhancement of hypocotyl elongation by LOV KELCH PROTEIN2 production is mediated by auxin and phytochrome-interacting factors in Arabidopsis thaliana.
    Plant Cell Rep., 2016. 35(2): p. 455-67
    [PMID:26601822]
  71. Yue J, et al.
    TOPP4 Regulates the Stability of PHYTOCHROME INTERACTING FACTOR5 during Photomorphogenesis in Arabidopsis.
    Plant Physiol., 2016. 170(3): p. 1381-97
    [PMID:26704640]
  72. Pedmale UV, et al.
    Cryptochromes Interact Directly with PIFs to Control Plant Growth in Limiting Blue Light.
    Cell, 2016. 164(1-2): p. 233-45
    [PMID:26724867]
  73. Pacín M,Semmoloni M,Legris M,Finlayson SA,Casal JJ
    Convergence of CONSTITUTIVE PHOTOMORPHOGENESIS 1 and PHYTOCHROME INTERACTING FACTOR signalling during shade avoidance.
    New Phytol., 2016. 211(3): p. 967-79
    [PMID:27105120]
  74. Fernández V,Takahashi Y,Le Gourrierec J,Coupland G
    Photoperiodic and thermosensory pathways interact through CONSTANS to promote flowering at high temperature under short days.
    Plant J., 2016. 86(5): p. 426-40
    [PMID:27117775]
  75. Martin G,Soy J,Monte E
    Genomic Analysis Reveals Contrasting PIFq Contribution to Diurnal Rhythmic Gene Expression in PIF-Induced and -Repressed Genes.
    Front Plant Sci, 2016. 7: p. 962
    [PMID:27458465]
  76. Gray JA,Shalit-Kaneh A,Chu DN,Hsu PY,Harmer SL
    The REVEILLE Clock Genes Inhibit Growth of Juvenile and Adult Plants by Control of Cell Size.
    Plant Physiol., 2017. 173(4): p. 2308-2322
    [PMID:28254761]
  77. Kasulin L, et al.
    A single haplotype hyposensitive to light and requiring strong vernalization dominates Arabidopsis thaliana populations in Patagonia, Argentina.
    Mol. Ecol., 2017. 26(13): p. 3389-3404
    [PMID:28316114]
  78. Wei Z, et al.
    Brassinosteroid Biosynthesis Is Modulated via a Transcription Factor Cascade of COG1, PIF4, and PIF5.
    Plant Physiol., 2017. 174(2): p. 1260-1273
    [PMID:28438793]
  79. Shor E,Paik I,Kangisser S,Green R,Huq E
    PHYTOCHROME INTERACTING FACTORS mediate metabolic control of the circadian system in Arabidopsis.
    New Phytol., 2017. 215(1): p. 217-228
    [PMID:28440582]
  80. Paik I,Kathare PK,Kim JI,Huq E
    Expanding Roles of PIFs in Signal Integration from Multiple Processes.
    Mol Plant, 2017. 10(8): p. 1035-1046
    [PMID:28711729]
  81. Swain S,Jiang HW,Hsieh HL
    FAR-RED INSENSITIVE 219/JAR1 Contributes to Shade Avoidance Responses of Arabidopsis Seedlings by Modulating Key Shade Signaling Components.
    Front Plant Sci, 2017. 8: p. 1901
    [PMID:29163619]