PIF1 (PHYTOCHROME INTERACTING FACTOR 1; also PIL5, PIF3-LIKE 5, bHLH015; At2g20180) is a nuclear basic helix-loop-helix transcription factor of the Arabidopsis thaliana PIF family (bHLH subgroup 15). It forms homodimers and heterodimers with other PIFs and with HFR1, binds G-box (CACGTG) elements in target promoters, and can activate or repress transcription. PIF1 is the PIF with the highest affinity for phytochromes: it binds the photoactivated Pfr forms of phyA and phyB through APA and APB motifs. Light-activated phytochromes trigger rapid PIF1 phosphorylation (with contributions from CK2, phytochromes and SPA1), followed by ubiquitination by CUL4-COP1-SPA and proteasomal degradation; under red light the half-life is about 1-2 min. In darkness PIF1 represses photomorphogenesis together with COP1-SPA, whose E3 ligase activity it enhances. It also restrains chlorophyll biosynthesis (regulating PORC, FeChII, HO3 and HEMB1), which prevents protochlorophyllide over-accumulation and photobleaching. PIF1 is the principal repressor of phytochrome-mediated seed germination: in imbibed seeds it binds the promoters of the DELLA genes GAI and RGA and of SOMNUS, and it acts indirectly on gibberellin and abscisic acid metabolism genes. It also inhibits hypocotyl negative gravitropism in darkness.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000976 transcription cis-regulatory region binding | IBA GO_REF:0000033 | ACCEPT | Summary: Transcription cis-regulatory region binding, propagated across PIFs. Directly supported for PIF1 by ChIP and EMSA at G-box elements (GAI, RGA, PORC, SOM). Reason: Core DNA-binding activity, directly demonstrated. Supporting Evidence: PMID:17449805 In vitro binding assays further confirmed that PIL5 directly and specifically bound G-box elements from the GAI and RGA promoters file:ARATH/PIF1/PIF1-deep-research-falcon.md PIF1 recognizes promoter DNA, particularly the **G-box sequence CACGTG**, through its bHLH transcription-factor machinery. |
| GO:0003677 DNA binding | IDA PMID:17449805 PIL5, a phytochrome-interacting bHLH protein, regulates gibb... | MODIFY | Summary: PIL5 binds G-box elements of the GAI and RGA promoters by ChIP and in vitro. Reason: Correct, but the binding is sequence-specific to cis-regulatory G-box elements; use the more specific term. Proposed replacements: transcription cis-regulatory region binding Supporting Evidence: PMID:17449805 PIL5 binds directly to GAI and RGA promoters but not to GA and ABA metabolic gene promoters |
| GO:0003700 DNA-binding transcription factor activity | IBA GO_REF:0000033 | ACCEPT | Summary: DNA-binding transcription factor activity propagated across the PIF clade. Reason: Core function, experimentally supported for PIF1. Supporting Evidence: PMID:18591656 PIF1 activates transcription of PORC in a G-box-dependent manner |
| GO:0003700 DNA-binding transcription factor activity | IDA PMID:21467583 ABI3 and PIL5 collaboratively activate the expression of SOM... | ACCEPT | Summary: PIL5 binds the SOMNUS promoter and activates SOM expression together with ABI3. Reason: Direct evidence for promoter binding and transcriptional activation. Supporting Evidence: PMID:21467583 ABI3 and PIL5 collaboratively activate the expression of SOM mRNA by directly binding to and interacting with each other at the SOM promoter |
| GO:0003700 DNA-binding transcription factor activity | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro-based DNA-binding transcription factor activity (bHLH PIF family). Reason: Consistent with experimental evidence. |
| GO:0003700 DNA-binding transcription factor activity | ISS PMID:11118137 Arabidopsis transcription factors: genome-wide comparative a... | ACCEPT | Summary: Genome-wide comparative survey of Arabidopsis transcription factors; bHLH classification. Reason: Consistent with direct experimental evidence; classification-level support. |
| GO:0003700 DNA-binding transcription factor activity | ISS PMID:12679534 The basic helix-loop-helix transcription factor family in pl... | ACCEPT | Summary: bHLH family genome-wide classification (subgroup 15). Reason: Consistent with direct experimental evidence. |
| GO:0003700 DNA-binding transcription factor activity | TAS PMID:16359394 PIF1 is regulated by light-mediated degradation through the ... | ACCEPT | Summary: PIF1 transcriptional activation activity noted in the LUC-PIF1 stability study. Reason: Consistent with direct experimental evidence. Supporting Evidence: PMID:16359394 the transcriptional activation activity of PIF1 is reduced in a phy-dependent manner |
| GO:0005515 protein binding | IPI PMID:15448264 Phytochrome-interacting factor 1 is a critical bHLH regulato... | MODIFY | Summary: Interaction with phyB (P14713) Pfr. Better captured by the specific term phytochrome binding. Reason: Use phytochrome binding. Proposed replacements: phytochrome binding Supporting Evidence: PMID:15448264 PIF1 interacts specifically with the photoactivated conformer of phytochromes A and B |
| GO:0005515 protein binding | IPI PMID:15486102 PIL5, a phytochrome-interacting basic helix-loop-helix prote... | MODIFY | Summary: Interaction with phyB Pfr. Reason: Use phytochrome binding. Proposed replacements: phytochrome binding Supporting Evidence: PMID:15486102 PIL5 preferentially interacts with the Pfr forms of Phytochrome A (PhyA) and Phytochrome B (PhyB) |
| GO:0005515 protein binding | IPI PMID:20093430 Transcriptional diversification and functional conservation ... | REMOVE | Summary: Interaction with DELLA RGL2 (Q8GXW1); DELLAs sequester PIFs. Reason: Bare protein-binding row removed per project policy; removal does not mean the interaction is false. DELLA-PIF interaction is a regulatory input onto PIF1, not an activity of PIF1. Supporting Evidence: PMID:20093430 both DELLA proteins display equivalent abilities to interact with PIF4 and with other bHLH transcription factors with a reported role in the control of cell growth and seed germination |
| GO:0005515 protein binding | IPI PMID:20093430 Transcriptional diversification and functional conservation ... | REMOVE | Summary: Interaction with DELLA RGA (Q9SLH3). Reason: Bare protein-binding row removed per project policy; removal does not mean the interaction is false. Regulatory input onto PIF1. |
| GO:0005515 protein binding | IPI PMID:21928113 Dimerization and blue light regulation of PIF1 interacting b... | MODIFY | Summary: PIF1-PIF3 heterodimerization; the heterodimer binds G-box DNA. Reason: Heterodimerization of bHLH proteins is captured by protein heterodimerization activity. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:21928113 PIF1-PIF3 heterodimer also bound to a G-box DNA sequence element in vitro |
| GO:0005515 protein binding | IPI PMID:21928113 Dimerization and blue light regulation of PIF1 interacting b... | MODIFY | Summary: Interaction with phyB. Reason: Use phytochrome binding. Proposed replacements: phytochrome binding |
| GO:0005515 protein binding | IPI PMID:21928113 Dimerization and blue light regulation of PIF1 interacting b... | MODIFY | Summary: Heterodimerization with the atypical HLH protein HFR1, which sequesters PIF1 from DNA. Reason: HLH-HLH heterodimerization. Proposed replacements: protein heterodimerization activity Supporting Evidence: PMID:21928113 PIF1 can form heterodimers with all other PIFs as well as with HFR1 |
| GO:0005515 protein binding | IPI PMID:22634759 Transposase-derived proteins FHY3/FAR1 interact with PHYTOCH... | REMOVE | Summary: PIF1 binds the DNA-binding domain of FHY3 and represses FHY3/FAR1-activated HEMB1 expression. Reason: Bare protein-binding row removed per project policy; removal does not mean the interaction is false. The functional consequence (repression of HEMB1) is covered by transcription regulation terms. Supporting Evidence: PMID:22634759 PHYTOCHROME-INTERACTING FACTOR1 physically interacts with the DNA binding domain of FHY3, thereby partly repressing FHY3/FAR1-activated HEMB1 expression |
| GO:0005515 protein binding | IPI PMID:22820378 Interaction between BZR1 and PIF4 integrates brassinosteroid... | REMOVE | Summary: BZR1 interacts with PIF1 (BiFC and pull-down) in a PIF4-focused study. Reason: Bare protein-binding row removed per project policy; removal does not mean the interaction is false. Supporting Evidence: PMID:22820378 indicating specific BZR1 interactions with PIF4 and PIF1 |
| GO:0005515 protein binding | IPI PMID:25944101 HEMERA Couples the Proteolysis and Transcriptional Activity ... | REMOVE | Summary: Interaction with HEMERA/pTAC12 (F4IHY7), a coactivator that couples PIF transactivation and degradation. Reason: Bare protein-binding row removed per project policy; removal does not mean the interaction is false. HMR acts on PIF1 as a coactivator; no informative PIF1 MF term beyond TF activity. Supporting Evidence: PMID:25944101 We show that HMR interacts with all PIFs |
| GO:0005515 protein binding | IPI PMID:32061894 PCH1 and PCHL Directly Interact with PIF1, Promote Its Degra... | REMOVE | Summary: Interaction with PCHL (O65680), which promotes PIF1 degradation and inhibits PIF1 DNA binding. Reason: Bare protein-binding row removed per project policy; removal does not mean the interaction is false. Regulatory input onto PIF1. Supporting Evidence: PMID:32061894 PCH1 and PCHL interact with PIF1 both in the dark and light, and regulate PIF1 abundance |
| GO:0005515 protein binding | IPI PMID:32061894 PCH1 and PCHL Directly Interact with PIF1, Promote Its Degra... | REMOVE | Summary: Interaction with PCH1 (Q84V03). Reason: Bare protein-binding row removed per project policy; removal does not mean the interaction is false. Regulatory input onto PIF1. |
| GO:0005634 nucleus | EXP PMID:15448264 Phytochrome-interacting factor 1 is a critical bHLH regulato... | ACCEPT | Summary: Nuclear localization of PIF1. Reason: PIF1 is a constitutively nuclear transcription factor. Supporting Evidence: PMID:18539749 constitutively nucleus-localized phy-interacting basic helix-loop-helix transcription factors (PIFs) |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: Nuclear activity propagated across PIFs. Reason: Consistent with direct evidence. |
| GO:0005634 nucleus | IDA PMID:15486102 PIL5, a phytochrome-interacting basic helix-loop-helix prote... | ACCEPT | Summary: PIL5 localizes to the nucleus. Reason: Direct evidence. Supporting Evidence: PMID:15486102 We showed that PIL5 localizes in the nucleus and preferentially interacts with the Pfr forms of both PhyA and PhyB |
| GO:0005634 nucleus | IDA PMID:16359394 PIF1 is regulated by light-mediated degradation through the ... | ACCEPT | Summary: Nuclear localization of LUC/GFP-PIF1. Reason: Consistent with other direct evidence. |
| GO:0005634 nucleus | IEA GO_REF:0000120 | ACCEPT | Summary: Combined automated nucleus annotation. Reason: Consistent with direct evidence. |
| GO:0005634 nucleus | ISM GO_REF:0000122 | ACCEPT | Summary: AtSubP nuclear prediction. Reason: Consistent with direct evidence. |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000002 | ACCEPT | Summary: Regulation of DNA-templated transcription (InterPro). Reason: Correct general process for a bHLH TF. |
| GO:0006355 regulation of DNA-templated transcription | IMP PMID:17449805 PIL5, a phytochrome-interacting bHLH protein, regulates gibb... | ACCEPT | Summary: PIL5 regulates GAI/RGA transcription; pil5 mutants and overexpressors alter DELLA expression. Reason: Direct target regulation demonstrated. Supporting Evidence: PMID:17449805 PIL5 increases the expression of two GA repressor (DELLA) genes, GA-INSENSITIVE (GAI) and REPRESSOR OF GA1-3 (RGA/RGA1), in darkness |
| GO:0006357 regulation of transcription by RNA polymerase II | IBA GO_REF:0000033 | ACCEPT | Summary: Regulation of transcription by RNA polymerase II propagated across PIFs. Reason: PIF1 regulates nuclear protein-coding genes; consistent with direct evidence. |
| GO:0006783 heme biosynthetic process | IMP PMID:18591656 PIF1 directly and indirectly regulates chlorophyll biosynthe... | KEEP AS NON CORE | Summary: pif1 alters expression of FeChII and HO3, heme-branch genes of the tetrapyrrole pathway. The effect on heme biosynthesis is transcriptional and indirect. Reason: acts_upstream_of_or_within is appropriate for a transcriptional regulator; non-core tetrapyrrole output. Supporting Evidence: PMID:18591656 PIF1 regulates expression of a discrete set of genes in the dark, including protochlorophyllide oxidoreductase (POR), ferrochelatase (FeChII), and heme oxygenase (HO3) |
| GO:0009408 response to heat | IEP PMID:23708772 Phytochrome-interacting factors have both shared and distinc... | MARK AS OVER ANNOTATED | Summary: Response to heat from a review comparing public expression data for PIF genes under stimuli (PIF1 transcript responsiveness). Reason: An expression change in a meta-analysis does not indicate that PIF1 functions in heat responses; PIF4, not PIF1, is the thermomorphogenesis PIF. |
| GO:0009409 response to cold | IEP PMID:23708772 Phytochrome-interacting factors have both shared and distinc... | MARK AS OVER ANNOTATED | Summary: Response to cold from the same expression meta-analysis. Note PIF1-related cold/light control of germination is mediated by SPATULA and PIL5 in seeds (Penfield et al. 2005), but that is a separate claim. Reason: Transcript responsiveness only. |
| GO:0009686 gibberellin biosynthetic process | IMP PMID:16740147 Light activates the degradation of PIL5 protein to promote s... | KEEP AS NON CORE | Summary: PIL5 represses GA3ox1/GA3ox2 and activates GA2ox2, lowering bioactive GA; acts_upstream_of_negative_effect is appropriate (indirect). Reason: Indirect transcriptional effect on GA metabolism; part of the seed germination role. Supporting Evidence: PMID:16740147 PIL5 repressed the expression of GA biosynthetic genes (GA3ox1 and GA3ox2), and activated the expression of a GA catabolic gene (GA2ox) |
| GO:0009733 response to auxin | IEP PMID:23708772 Phytochrome-interacting factors have both shared and distinc... | MARK AS OVER ANNOTATED | Summary: Response to auxin from expression meta-analysis. Reason: Transcript responsiveness only. |
| GO:0009737 response to abscisic acid | IEP PMID:23708772 Phytochrome-interacting factors have both shared and distinc... | MARK AS OVER ANNOTATED | Summary: Response to ABA from expression meta-analysis. PIF1 does regulate ABA metabolism genes in seeds (Oh et al. 2007), but the IEP annotation is about PIF1 transcript change. Reason: Transcript responsiveness only. |
| GO:0009740 gibberellic acid mediated signaling pathway | IMP PMID:18053005 Gibberellins modulate light signaling pathways to prevent Ar... | KEEP AS NON CORE | Summary: GA-light crosstalk paper; GA signaling regulates PIF activity. The abstract focuses on PIF3; the curator presumably saw PIF1 data in the full text. Reason: Experimental; PIF1 also directly regulates DELLA gene expression (GAI, RGA), linking it to GA signaling. Non-core. Supporting Evidence: PMID:17449805 PIL5, a phytochrome-interacting bHLH protein, regulates gibberellin responsiveness by binding directly to the GAI and RGA promoters |
| GO:0009959 negative gravitropism | IMP PMID:16740147 Light activates the degradation of PIL5 protein to promote s... | KEEP AS NON CORE | Summary: PIL5 inhibits hypocotyl negative gravitropism in darkness. Reason: Established PIF1-dependent phenotype; secondary to germination and de-etiolation roles. Supporting Evidence: PMID:15486102 PIL5 is a negative factor in Phy-mediated promotion of seed germination, inhibition of hypocotyl negative gravitropism, and inhibition of hypocotyl elongation |
| GO:0009959 negative gravitropism | TAS PMID:16359394 PIF1 is regulated by light-mediated degradation through the ... | KEEP AS NON CORE | Summary: Traceable author statement on gravitropism. Reason: Consistent with IMP evidence. |
| GO:0010017 red or far-red light signaling pathway | IEA GO_REF:0000117 | ACCEPT | Summary: Red or far-red light signaling pathway (ARBA). Reason: PIF1 is a direct Pfr-phytochrome partner acting in both phyA and phyB signaling. Supporting Evidence: PMID:18539749 phyA plays a dominant role in regulating the degradation of PIF1 following initial light exposure |
| GO:0010029 regulation of seed germination | TAS PMID:16359394 PIF1 is regulated by light-mediated degradation through the ... | MODIFY | Summary: Regulation of seed germination (author statement). Reason: PIF1 is a negative regulator; use the directional child. Proposed replacements: negative regulation of seed germination |
| GO:0010099 regulation of photomorphogenesis | TAS PMID:16359394 PIF1 is regulated by light-mediated degradation through the ... | MODIFY | Summary: Regulation of photomorphogenesis (author statement). Reason: PIF1 negatively regulates photomorphogenesis. Proposed replacements: negative regulation of photomorphogenesis |
| GO:0010100 negative regulation of photomorphogenesis | IMP PMID:18539749 Light-induced phosphorylation and degradation of the negativ... | ACCEPT | Summary: Light-stable truncated PIF1 causes photomorphogenic changes; PIF1 represses photomorphogenesis. Reason: Core role, supported by multiple genetic studies (pif1 cop1 synergy, Xu et al. 2014). Supporting Evidence: PMID:24858936 PIF1 forms complexes with COP1, HY5, and SPA1 and enhances the substrate recruitment and autoubiquitylation and transubiquitylation activities of COP1 |
| GO:0010161 red light signaling pathway | IBA GO_REF:0000033 | ACCEPT | Summary: Red light signaling pathway propagated across PIFs. Reason: PIF1 is the most red-light-labile PIF; direct phyB partner. Supporting Evidence: PMID:18539749 PIF1 is rapidly phosphorylated and ubiquitinated under red and far-red light before being degraded with a half-life of approximately 1 to 2 min under red light |
| GO:0010161 red light signaling pathway | IDA PMID:18539749 Light-induced phosphorylation and degradation of the negativ... | ACCEPT | Summary: Red-light-induced phy-dependent phosphorylation and degradation of PIF1. Reason: Direct evidence that PIF1 is a target within red light signaling. Supporting Evidence: PMID:18539749 phy interaction is necessary but not sufficient for the light-induced phosphorylation and degradation of PIF1 |
| GO:0010187 negative regulation of seed germination | IMP PMID:16303558 Cold and light control seed germination through the bHLH tra... | ACCEPT | Summary: PIL5 represses seed germination and GA3ox expression in the dark. Reason: Core physiological role of PIF1. Supporting Evidence: PMID:16303558 We also show that the related protein PIL5 represses seed germination and GA3ox expression in the dark |
| GO:0010313 phytochrome binding | IDA PMID:15486102 PIL5, a phytochrome-interacting basic helix-loop-helix prote... | ACCEPT | Summary: PIL5 binds Pfr forms of phyA and phyB. Reason: Defining PIF1 activity linking phytochrome perception to transcription. Supporting Evidence: PMID:15486102 PIL5 preferentially interacts with the Pfr forms of Phytochrome A (PhyA) and Phytochrome B (PhyB) |
| GO:0015995 chlorophyll biosynthetic process | IMP PMID:15448264 Phytochrome-interacting factor 1 is a critical bHLH regulato... | KEEP AS NON CORE | Summary: pif1 mutants over-accumulate protochlorophyllide in darkness and bleach in light; PIF1 negatively regulates chlorophyll biosynthesis. Reason: acts_upstream_of_or_within appropriate for transcriptional repression of the pathway; important output, but PIF1 is a regulator not a participant. Supporting Evidence: PMID:15448264 pif1 mutant seedlings accumulate excess free protochlorophyllide when grown in the dark, with consequent lethal bleaching upon exposure to light |
| GO:0042802 identical protein binding | IPI PMID:21928113 Dimerization and blue light regulation of PIF1 interacting b... | MODIFY | Summary: PIF1 homodimerization (yeast two-hybrid). Reason: bHLH homodimerization is better captured by protein homodimerization activity. Proposed replacements: protein homodimerization activity Supporting Evidence: PMID:21928113 identified a group of proteins including PIF1 itself, PIF3 and long hypocotyl in far-red 1 (HFR1) |
| GO:0046983 protein dimerization activity | IEA GO_REF:0000002 | ACCEPT | Summary: Protein dimerization activity from the bHLH domain. Reason: bHLH proteins bind DNA as dimers; supported by homo- and heterodimerization data. |
| GO:0097027 ubiquitin-protein transferase activator activity | IDA PMID:24858936 PHYTOCHROME INTERACTING FACTOR1 Enhances the E3 Ligase Activ... | NEW | Summary: In vitro, PIF1 increases COP1-HY5 association, COP1 autoubiquitylation and COP1 transubiquitylation of HY5 in a concentration-dependent manner; in darkness PIF1 acts as a cofactor of the COP1-SPA E3 ligase. Reason: Direct biochemical evidence for an E3-activator activity of PIF1 not represented in GOA. This is the same activity term used for SPA1's stimulation of COP1, and the evidence is of the same kind (in vitro ubiquitylation assays with the purified cofactor). Single-study evidence, so it is recorded as a secondary core function alongside the transcription factor activity. Supporting Evidence: PMID:24858936 PIF1 forms complexes with COP1, HY5, and SPA1 and enhances the substrate recruitment and autoubiquitylation and transubiquitylation activities of COP1 PMID:24858936 PIF1 enhances the transubiquitylation of HY5 by COP1 ∼2- to 4-fold in a concentration-dependent manner |
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Download this section (compressed HTML)Q: Which kinase(s) perform the rapid light-induced PIF1 phosphorylation in vivo: phytochrome itself, SPA1, CK2 or PPKs? What is the relative contribution of each?
Q: How does PIF1 switch between activator (SOM, GAI/RGA, PORC) and repressor (GA3ox, photosynthesis genes) roles at different targets?
Experiment: Map in vivo PIF1 phosphosites under red light in spaQ, ck2 and ppk mutant backgrounds by targeted phosphoproteomics, and test phospho-null/phospho-mimic PIF1 variants for degradation kinetics and germination phenotypes.
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