BES1 (BRI1-EMS-SUPPRESSOR 1; also BZR2; At1g19350) is a plant-specific BZR/BES1-family transcription factor and, together with its closest homolog BZR1, the principal nuclear effector of brassinosteroid (BR) signalling. In the absence of BR, the GSK3-like kinase BIN2 phosphorylates BES1 on multiple sites, which inhibits DNA binding, promotes 14-3-3 binding, cytoplasmic retention and nuclear export, and destabilizes the protein. BR perception inactivates BIN2 and PP2A/BSU1 phosphatases dephosphorylate BES1, which then accumulates in the nucleus. Nuclear BES1 binds BRRE and E-box elements in thousands of target promoters, cooperating with bHLH partners such as BIM1 to activate BR-induced genes and with repressors such as MYBL2 to repress BR-repressed genes; it also recruits chromatin regulators (ELF6, REF6, SDG8) and the elongation factor IWS1. BES1 controls cell elongation, male fertility, root quiescent-centre division (via BRAVO), flavonol accumulation and UV-B responses, and contributes to immunity after phosphorylation by MPK6. The semidominant bes1-D (P233L) mutation stabilizes BES1 and causes constitutive BR responses. Arabidopsis thaliana also expresses a long isoform (BES1-L) with an extra nuclear localization signal.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000978 RNA polymerase II cis-regulatory region sequence-specific DNA binding | IDA PMID:24981610 Regulation of plant stem cell quiescence by a brassinosteroi... | ACCEPT | Summary: BES1 binds the BRAVO promoter. Reason: Sequence-specific cis-regulatory DNA binding. Supporting Evidence: PMID:24981610 BR-regulated transcription factor BES1 (BRI1-EMS SUPRESSOR 1) directly represses and physically interacts with BRAVO in vivo |
| GO:0000987 cis-regulatory region sequence-specific DNA binding | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference of cis-regulatory DNA binding for BZR family. Reason: BES1 is an experimental source for this node; BZR family binds BRRE/E-box elements. Supporting Evidence: PMID:15680330 BES1 interacts with a basic helix-loop-helix protein, BIM1, to synergistically bind to E box (CANNTG) sequences present in many BR-induced promoters. |
| GO:0003677 DNA binding | IDA PMID:20231470 Brassinosteroids control male fertility by regulating the ex... | ACCEPT | Summary: BES1 binds target promoters (ChIP). Reason: Correct, though less specific than cis-regulatory sequence-specific DNA binding. Supporting Evidence: PMID:20231470 BES1, an important transcription factor for brassinosteroid signaling, could directly bind to the promoter regions of genes encoding transcription factors essential for anther and pollen development |
| GO:0003677 DNA binding | IDA PMID:24981610 Regulation of plant stem cell quiescence by a brassinosteroi... | ACCEPT | Summary: BES1 binds target promoters (ChIP). Reason: Correct, though less specific than cis-regulatory sequence-specific DNA binding. Supporting Evidence: PMID:24981610 BR-regulated transcription factor BES1 (BRI1-EMS SUPRESSOR 1) directly represses and physically interacts with BRAVO in vivo |
| GO:0003700 DNA-binding transcription factor activity | IBA GO_REF:0000033 | ACCEPT | Summary: BES1 is a DNA-binding transcription factor of the plant-specific BZR family. Reason: Core molecular function. Supporting Evidence: PMID:15680330 establish that BES1 is a transcription factor that binds to and activates BR target gene promoters both in vitro and in vivo |
| GO:0003700 DNA-binding transcription factor activity | IDA PMID:15680330 A new class of transcription factors mediates brassinosteroi... | ACCEPT | Summary: BES1 is a DNA-binding transcription factor of the plant-specific BZR family. Reason: Core molecular function. Supporting Evidence: PMID:15680330 establish that BES1 is a transcription factor that binds to and activates BR target gene promoters both in vitro and in vivo |
| GO:0003700 DNA-binding transcription factor activity | IDA PMID:24981610 Regulation of plant stem cell quiescence by a brassinosteroi... | ACCEPT | Summary: BES1 is a DNA-binding transcription factor of the plant-specific BZR family. Reason: Core molecular function. Supporting Evidence: PMID:24981610 BR-regulated transcription factor BES1 (BRI1-EMS SUPRESSOR 1) directly represses and physically interacts with BRAVO in vivo |
| GO:0003700 DNA-binding transcription factor activity | IEA GO_REF:0000002 | ACCEPT | Summary: BES1 is a DNA-binding transcription factor of the plant-specific BZR family. Reason: Core molecular function. Supporting Evidence: PMID:15680330 establish that BES1 is a transcription factor that binds to and activates BR target gene promoters both in vitro and in vivo |
| GO:0005515 protein binding | IPI PMID:12007405 BES1 accumulates in the nucleus in response to brassinostero... | REMOVE | Summary: IPI with BIN2. Reason: Generic protein binding is uninformative; removal does not imply the interaction is false (the partner is noted in the description/notes). Supporting Evidence: PMID:12007405 BES1 is phosphorylated and appears to be destabilized by the glycogen synthase kinase-3 (GSK-3) BIN2, a negative regulator of the BR pathway. |
| GO:0005515 protein binding | IPI PMID:12427989 Two putative BIN2 substrates are nuclear components of brass... | REMOVE | Summary: IPI with BRI1. Reason: Generic protein binding is uninformative; removal does not imply the interaction is false (the partner is noted in the description/notes). Supporting Evidence: PMID:12427989 Five independent bes1 alleles containing the same proline-233-Leu mutation were identified as semidominant suppressors of two different bri1 mutations. |
| GO:0005515 protein binding | IPI PMID:15680330 A new class of transcription factors mediates brassinosteroi... | MODIFY | Summary: IPI with BIM1, a DNA-binding transcription factor partner of BES1. Reason: Generic protein binding is uninformative; the partner is a transcription factor with which BES1 co-regulates target genes. Proposed replacements: DNA-binding transcription factor binding Supporting Evidence: PMID:15680330 BES1 interacts with a basic helix-loop-helix protein, BIM1, to synergistically bind to E box (CANNTG) sequences present in many BR-induced promoters. |
| GO:0005515 protein binding | IPI PMID:15680330 A new class of transcription factors mediates brassinosteroi... | MODIFY | Summary: IPI with BIM1, a DNA-binding transcription factor partner of BES1. Reason: Generic protein binding is uninformative; the partner is a transcription factor with which BES1 co-regulates target genes. Proposed replacements: DNA-binding transcription factor binding Supporting Evidence: PMID:15680330 BES1 interacts with a basic helix-loop-helix protein, BIM1, to synergistically bind to E box (CANNTG) sequences present in many BR-induced promoters. |
| GO:0005515 protein binding | IPI PMID:18467490 Modulation of brassinosteroid-regulated gene expression by J... | REMOVE | Summary: IPI with ELF6 (histone demethylase). Reason: Generic protein binding is uninformative; removal does not imply the interaction is false (the partner is noted in the description/notes). Supporting Evidence: PMID:18467490 we identified two BES1-interacting proteins, ELF6 (early flowering 6) and its homolog REF6 (relative of early flowering 6), both of which are Jumonji N/C (JmjN/C) domain-containing proteins |
| GO:0005515 protein binding | IPI PMID:18467490 Modulation of brassinosteroid-regulated gene expression by J... | REMOVE | Summary: IPI with REF6 (histone demethylase). Reason: Generic protein binding is uninformative; removal does not imply the interaction is false (the partner is noted in the description/notes). Supporting Evidence: PMID:18467490 we identified two BES1-interacting proteins, ELF6 (early flowering 6) and its homolog REF6 (relative of early flowering 6), both of which are Jumonji N/C (JmjN/C) domain-containing proteins |
| GO:0005515 protein binding | IPI PMID:20139304 Arabidopsis IWS1 interacts with transcription factor BES1 an... | REMOVE | Summary: IPI with IWS1 (transcription elongation factor). Reason: Generic protein binding is uninformative; removal does not imply the interaction is false (the partner is noted in the description/notes). Supporting Evidence: PMID:20139304 Moreover, AtIWS1 interacts with BES1 both in vitro and in vivo. |
| GO:0005515 protein binding | IPI PMID:20139304 Arabidopsis IWS1 interacts with transcription factor BES1 an... | REMOVE | Summary: IPI with IWS2. Reason: Generic protein binding is uninformative; removal does not imply the interaction is false. The cached abstract describes the BES1-IWS1 interaction only; the IWS2 interaction data are in the full text (not cached), so no supporting quote is given and the curator's observation is not disputed. |
| GO:0005515 protein binding | IPI PMID:23169658 MYBL2 is a substrate of GSK3-like kinase BIN2 and acts as a ... | MODIFY | Summary: IPI with MYBL2 (transcriptional repressor), a DNA-binding transcription factor partner of BES1. Reason: Generic protein binding is uninformative; the partner is a transcription factor with which BES1 co-regulates target genes. Proposed replacements: DNA-binding transcription factor binding Supporting Evidence: PMID:23169658 Here, we show that BES1 interacts with myeloblastosis family transcription factor-like 2 (MYBL2), a transcription repressor, to down-regulate BR-repressed gene expression. |
| GO:0005515 protein binding | IPI PMID:24662460 Plant GSK3 proteins regulate xylem cell differentiation down... | REMOVE | Summary: IPI with TDR receptor kinase. Reason: Generic protein binding is uninformative; removal does not imply the interaction is false. The cached abstract describes TDR interacting with and activating GSK3s, with BES1 acting downstream; the BES1-TDR interaction data are in the full text (not cached), so no supporting quote is given and the curator's observation is not disputed. |
| GO:0005515 protein binding | IPI PMID:24838002 Histone lysine methyltransferase SDG8 is involved in brassin... | REMOVE | Summary: IPI with SDG8/ASHH2 (histone methyltransferase). Reason: Generic protein binding is uninformative; removal does not imply the interaction is false (the partner is noted in the description/notes). Supporting Evidence: PMID:24838002 BES1 interacts with SDG8, directly or indirectly through IWS1, a transcription elongation factor involved in BR-regulated gene expression. |
| GO:0005515 protein binding | IPI PMID:24981610 Regulation of plant stem cell quiescence by a brassinosteroi... | MODIFY | Summary: IPI with BRAVO/MYB56, a DNA-binding transcription factor partner of BES1. Reason: Generic protein binding is uninformative; the partner is a transcription factor with which BES1 co-regulates target genes. Proposed replacements: DNA-binding transcription factor binding Supporting Evidence: PMID:24981610 BR-regulated transcription factor BES1 (BRI1-EMS SUPRESSOR 1) directly represses and physically interacts with BRAVO in vivo |
| GO:0005515 protein binding | IPI PMID:28576847 Arabidopsis WRKY46, WRKY54, and WRKY70 Transcription Factors... | MODIFY | Summary: IPI with WRKY54, a DNA-binding transcription factor partner of BES1. Reason: Generic protein binding is uninformative; the partner is a transcription factor with which BES1 co-regulates target genes. Proposed replacements: DNA-binding transcription factor binding Supporting Evidence: PMID:28576847 WRKY54 directly interacts with BES1 to cooperatively regulate the expression of target genes. PMID:28576847 we found that three Arabidopsis thaliana group III WRKY transcription factors, WRKY46, WRKY54, and WRKY70, are involved in both BR-regulated plant growth and drought response |
| GO:0005515 protein binding | IPI PMID:28576847 Arabidopsis WRKY46, WRKY54, and WRKY70 Transcription Factors... | MODIFY | Summary: IPI with WRKY70, a DNA-binding transcription factor partner of BES1. Reason: Generic protein binding is uninformative; WRKY70 is a group III WRKY transcription factor that acts with BES1 in BR-regulated growth, so DNA-binding transcription factor binding is the informative term. The cached abstract states direct interaction for WRKY54 only; the WRKY70 interaction data are in the full text (not cached) and are deferred to the curator. Proposed replacements: DNA-binding transcription factor binding Supporting Evidence: PMID:28576847 we found that three Arabidopsis thaliana group III WRKY transcription factors, WRKY46, WRKY54, and WRKY70, are involved in both BR-regulated plant growth and drought response |
| GO:0005515 protein binding | IPI PMID:28576847 Arabidopsis WRKY46, WRKY54, and WRKY70 Transcription Factors... | MODIFY | Summary: IPI with WRKY46, a DNA-binding transcription factor partner of BES1. Reason: Generic protein binding is uninformative; WRKY46 is a group III WRKY transcription factor that acts with BES1 in BR-regulated growth, so DNA-binding transcription factor binding is the informative term. The cached abstract states direct interaction for WRKY54 only; the WRKY46 interaction data are in the full text (not cached) and are deferred to the curator. Proposed replacements: DNA-binding transcription factor binding Supporting Evidence: PMID:28576847 we found that three Arabidopsis thaliana group III WRKY transcription factors, WRKY46, WRKY54, and WRKY70, are involved in both BR-regulated plant growth and drought response |
| GO:0005634 nucleus | EXP PMID:12007405 BES1 accumulates in the nucleus in response to brassinostero... | ACCEPT | Summary: Dephosphorylated BES1 accumulates in the nucleus. Reason: Core location. Supporting Evidence: PMID:12007405 BES1 accumulates in the nucleus in response to BRs. |
| GO:0005634 nucleus | EXP PMID:24838002 Histone lysine methyltransferase SDG8 is involved in brassin... | ACCEPT | Summary: Dephosphorylated BES1 accumulates in the nucleus. Reason: Core location. Supporting Evidence: PMID:12007405 BES1 accumulates in the nucleus in response to BRs. |
| GO:0005634 nucleus | IBA GO_REF:0000033 | ACCEPT | Summary: Dephosphorylated BES1 accumulates in the nucleus. Reason: Core location. Supporting Evidence: PMID:12007405 BES1 accumulates in the nucleus in response to BRs. |
| GO:0005634 nucleus | IDA PMID:12427989 Two putative BIN2 substrates are nuclear components of brass... | ACCEPT | Summary: Dephosphorylated BES1 accumulates in the nucleus. Reason: Core location. Supporting Evidence: PMID:12007405 BES1 accumulates in the nucleus in response to BRs. |
| GO:0005634 nucleus | IDA PMID:24981610 Regulation of plant stem cell quiescence by a brassinosteroi... | ACCEPT | Summary: Dephosphorylated BES1 accumulates in the nucleus. Reason: Core location. Supporting Evidence: PMID:24981610 BR-regulated transcription factor BES1 (BRI1-EMS SUPRESSOR 1) directly represses and physically interacts with BRAVO in vivo |
| GO:0005634 nucleus | IDA PMID:25649439 A recently evolved isoform of the transcription factor BES1 ... | ACCEPT | Summary: Dephosphorylated BES1 accumulates in the nucleus. Reason: Core location. Supporting Evidence: PMID:25649439 The BES1-L isoform contains an additional N-terminal bipartite nuclear localization signal, which strongly promotes its nuclear localization. |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: Dephosphorylated BES1 accumulates in the nucleus. Reason: Core location. Supporting Evidence: PMID:12007405 BES1 accumulates in the nucleus in response to BRs. |
| GO:0005737 cytoplasm | EXP PMID:12007405 BES1 accumulates in the nucleus in response to brassinostero... | ACCEPT | Summary: Phosphorylated BES1 is retained in the cytoplasm via 14-3-3 binding. Reason: Cytoplasmic pool is the inactive, BIN2-phosphorylated form. Supporting Evidence: PMID:17681130 promoting binding to the 14-3-3 proteins, which increases cytoplasmic retention of BZR1 and BZR2/BES1 PMID:20387034 phosphorylate BES1 and induce its nuclear export by regulating its binding affinity with 14-3-3 proteins |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: Phosphorylated BES1 is retained in the cytoplasm via 14-3-3 binding. Reason: Cytoplasmic pool is the inactive, BIN2-phosphorylated form. Supporting Evidence: PMID:17681130 promoting binding to the 14-3-3 proteins, which increases cytoplasmic retention of BZR1 and BZR2/BES1 PMID:20387034 phosphorylate BES1 and induce its nuclear export by regulating its binding affinity with 14-3-3 proteins |
| GO:0005737 cytoplasm | ISM GO_REF:0000122 | ACCEPT | Summary: Phosphorylated BES1 is retained in the cytoplasm via 14-3-3 binding. Reason: Cytoplasmic pool is the inactive, BIN2-phosphorylated form. Supporting Evidence: PMID:17681130 promoting binding to the 14-3-3 proteins, which increases cytoplasmic retention of BZR1 and BZR2/BES1 PMID:20387034 phosphorylate BES1 and induce its nuclear export by regulating its binding affinity with 14-3-3 proteins |
| GO:0005829 cytosol | IDA PMID:17681130 An essential role for 14-3-3 proteins in brassinosteroid sig... | ACCEPT | Summary: Phosphorylated BES1 is retained in the cytosol by 14-3-3 proteins. Reason: Direct evidence. Supporting Evidence: PMID:17681130 promoting binding to the 14-3-3 proteins, which increases cytoplasmic retention of BZR1 and BZR2/BES1 |
| GO:0006351 DNA-templated transcription | IEA GO_REF:0000002 | MODIFY | Summary: InterPro-based DNA-templated transcription. Reason: Transcription factors regulate rather than carry out transcription; regulation of DNA-templated transcription is appropriate. Proposed replacements: regulation of DNA-templated transcription Supporting Evidence: PMID:15680330 establish that BES1 is a transcription factor that binds to and activates BR target gene promoters both in vitro and in vivo |
| GO:0006355 regulation of DNA-templated transcription | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA regulation of transcription. Reason: Consistent. Supporting Evidence: PMID:15680330 establish that BES1 is a transcription factor that binds to and activates BR target gene promoters both in vitro and in vivo |
| GO:0006355 regulation of DNA-templated transcription | TAS PMID:11970900 Nuclear-localized BZR1 mediates brassinosteroid-induced grow... | ACCEPT | Summary: BES1 regulates transcription of BR-responsive genes. Reason: Core process of a DNA-binding transcription factor. Supporting Evidence: PMID:15680330 establish that BES1 is a transcription factor that binds to and activates BR target gene promoters both in vitro and in vivo |
| GO:0009416 response to light stimulus | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Phylogenetic inference of response to light for BES1/BZR1 node. Reason: BES1/BZR1 integrate BR with light (photomorphogenesis) and UV-B responses, but this is a secondary output. Supporting Evidence: PMID:32796123 BES1 directly binds to the promoters of these MYBs in a BR-enhanced manner to repress their expression, thereby reducing flavonol accumulation. |
| GO:0009507 chloroplast | ISM GO_REF:0000122 | REMOVE | Summary: AtSubP prediction of chloroplast localization. Reason: No experimental support; BES1 is a nucleocytoplasmic transcription factor without a transit peptide function. Supporting Evidence: PMID:20387034 phosphorylate BES1 and induce its nuclear export by regulating its binding affinity with 14-3-3 proteins |
| GO:0009650 UV protection | IDA PMID:32796123 Brassinosteroid-Activated BRI1-EMS-SUPPRESSOR 1 Inhibits Fla... | KEEP AS NON CORE | Summary: BES1 represses MYB11/12/111 and flavonol biosynthesis, reducing UV-B protection. Reason: Real target-gene output (acts upstream of or within); BES1 actually antagonises UV protection to favour growth. Supporting Evidence: PMID:32796123 BES1 directly binds to the promoters of these MYBs in a BR-enhanced manner to repress their expression, thereby reducing flavonol accumulation. |
| GO:0009742 brassinosteroid mediated signaling pathway | IBA GO_REF:0000033 | ACCEPT | Summary: BES1 mediates BR signalling outputs. Reason: Core process. Supporting Evidence: PMID:12007405 BES1 accumulates in the nucleus in response to BRs. |
| GO:0009742 brassinosteroid mediated signaling pathway | IEA GO_REF:0000002 | ACCEPT | Summary: BES1 mediates BR signalling outputs. Reason: Core process. Supporting Evidence: PMID:12007405 BES1 accumulates in the nucleus in response to BRs. |
| GO:0009742 brassinosteroid mediated signaling pathway | IGI PMID:12007405 BES1 accumulates in the nucleus in response to brassinostero... | ACCEPT | Summary: BES1 acts in BR signalling downstream of BIN2. Reason: Core process. Supporting Evidence: PMID:12007405 BES1 accumulates in the nucleus in response to BRs. PMID:12007405 BES1 is phosphorylated and appears to be destabilized by the glycogen synthase kinase-3 (GSK-3) BIN2, a negative regulator of the BR pathway. |
| GO:0009742 brassinosteroid mediated signaling pathway | IMP PMID:24981610 Regulation of plant stem cell quiescence by a brassinosteroi... | ACCEPT | Summary: BES1 mediates BR signalling outputs. Reason: Core process. Supporting Evidence: PMID:12007405 BES1 accumulates in the nucleus in response to BRs. |
| GO:0042742 defense response to bacterium | IMP PMID:25609555 The Arabidopsis transcription factor BRASSINOSTEROID INSENSI... | KEEP AS NON CORE | Summary: bes1 mutants are compromised in resistance to Pseudomonas syringae. Reason: Secondary immune role via MPK6 phosphorylation. Supporting Evidence: PMID:25609555 bes1 loss-of-function mutants display compromised resistance to bacterial pathogen Pseudomonas syringae pv tomato DC3000 |
| GO:0045892 negative regulation of DNA-templated transcription | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference of negative regulation of transcription (BES1/BZR1 node). Reason: Supported by direct repression evidence for BES1. Supporting Evidence: PMID:24981610 BR-regulated transcription factor BES1 (BRI1-EMS SUPRESSOR 1) directly represses and physically interacts with BRAVO in vivo |
| GO:0045892 negative regulation of DNA-templated transcription | IDA PMID:24981610 Regulation of plant stem cell quiescence by a brassinosteroi... | ACCEPT | Summary: BES1 directly represses BRAVO. Reason: BES1 acts as repressor on a large subset of targets (BRAVO, MYB11/12/111, BR biosynthetic genes). Supporting Evidence: PMID:24981610 BR-regulated transcription factor BES1 (BRI1-EMS SUPRESSOR 1) directly represses and physically interacts with BRAVO in vivo PMID:32796123 BES1 directly binds to the promoters of these MYBs in a BR-enhanced manner to repress their expression, thereby reducing flavonol accumulation. |
| GO:0071367 cellular response to brassinosteroid stimulus | IMP PMID:24981610 Regulation of plant stem cell quiescence by a brassinosteroi... | KEEP AS NON CORE | Summary: bes1 mutants alter root QC response to BR. Reason: Correct but overlaps the more specific BR signalling annotation. Supporting Evidence: PMID:24981610 BR-regulated transcription factor BES1 (BRI1-EMS SUPRESSOR 1) directly represses and physically interacts with BRAVO in vivo |
| GO:1904961 quiescent center organization | IMP PMID:24981610 Regulation of plant stem cell quiescence by a brassinosteroi... | KEEP AS NON CORE | Summary: BES1-BRAVO switch modulates QC divisions. Reason: Context-specific developmental output. Supporting Evidence: PMID:24981610 BR-regulated transcription factor BES1 (BRI1-EMS SUPRESSOR 1) directly represses and physically interacts with BRAVO in vivo |
| GO:0045893 positive regulation of DNA-templated transcription | IDA PMID:15680330 A new class of transcription factors mediates brassinosteroi... | NEW | Summary: BES1 binds to and activates BR target gene promoters, alone and synergistically with BIM1. Reason: GOA carries only negative regulation of transcription for BES1, yet BES1 is a DNA-binding transcription factor that itself activates BR-induced target promoters in vitro and in vivo, and recruits coactivators (ELF6/REF6, IWS1) to these genes. BES1 performs the step (promoter binding and activation), so the participation test is met; activation and repression both occur, on different target sets. Supporting Evidence: PMID:15680330 establish that BES1 is a transcription factor that binds to and activates BR target gene promoters both in vitro and in vivo |
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Download this section (compressed HTML)Q: To what extent are BES1 and BZR1 functionally interchangeable in vivo, given their differing preference for activation versus repression?
Q: What is the functional significance of the accession-specific BES1-L isoform for BR responses in natural populations?
Experiment: ChIP-seq of BES1-S and BES1-L in bes1 bzr1 backgrounds with and without BR to compare their target repertoires and BIM1 dependence.
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