NINJA

Summary: NINJA binds TOPLESS and TPL-related corepressors through its EAR motif in domain A.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor (TPL/TPR are Groucho/Tup1-type corepressors).

Proposed replacements: transcription corepressor binding

Summary: NINJA binds the TIFY motif of most JAZ repressors.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor. JAZ proteins act as transcriptional corepressors of MYC transcription factors and recruit TOPLESS via NINJA.

Proposed replacements: transcription corepressor binding

Summary: NINJA binds the TIFY motif of most JAZ repressors.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor. JAZ proteins act as transcriptional corepressors of MYC transcription factors and recruit TOPLESS via NINJA.

Proposed replacements: transcription corepressor binding

Summary: The partner here is JAZ8/TIFY5A (AT1G30135), one of the JAZ proteins for which the assays of PMID:20360743 disagree about NINJA binding (pull-down positive, Y2H negative; JAZ11 and JAZ12 disagree the other way), whose NINJA binding is weak in a later pull-down, and whose repression does not use NINJA.

Reason: The interaction rests on an in vitro MBP pull-down (NINJA was pulled down by all JAZ-MBP fusions except JAZ7, JAZ11 and JAZ12), while the same paper's systematic Y2H found NINJA binding most JAZ proteins "except JAZ7 and JAZ8", and UniProt's curated NINJA interactor list omits TIFY5A/JAZ8. The binding is therefore not refuted, but generic protein binding is uninformative, and the functional reading used for the other JAZ partners (NINJA as the corepressor adaptor that bridges the JAZ ZIM domain to TOPLESS, hence transcription corepressor binding) does not apply to JAZ8. JAZ8 carries its own N-terminal EAR motif that recruits TOPLESS directly, and JAZ8-mediated repression does not require the ZIM domain that recruits NINJA in other JAZ proteins (PMID:22327740). That paper's own pull-down recovered much less NINJA with JAZ8 than with JAZ10.1, though more than with the MBP control. With no informative molecular-function term to convert to, the uninformative protein binding term is removed rather than converted to transcription corepressor binding. Removal concerns only the uninformative protein binding term, not the validity of the reported interaction.

Summary: NINJA binds the TIFY motif of most JAZ repressors.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor. JAZ proteins act as transcriptional corepressors of MYC transcription factors and recruit TOPLESS via NINJA.

Proposed replacements: transcription corepressor binding

Summary: NINJA binds the TIFY motif of most JAZ repressors.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor. JAZ proteins act as transcriptional corepressors of MYC transcription factors and recruit TOPLESS via NINJA.

Proposed replacements: transcription corepressor binding

Summary: NINJA binds the TIFY motif of most JAZ repressors.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor. JAZ proteins act as transcriptional corepressors of MYC transcription factors and recruit TOPLESS via NINJA.

Proposed replacements: transcription corepressor binding

Summary: NINJA binds the TIFY motif of most JAZ repressors.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor. JAZ proteins act as transcriptional corepressors of MYC transcription factors and recruit TOPLESS via NINJA.

Proposed replacements: transcription corepressor binding

Summary: NINJA binds TOPLESS and TPL-related corepressors through its EAR motif in domain A.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor (TPL/TPR are Groucho/Tup1-type corepressors).

Proposed replacements: transcription corepressor binding

Summary: NINJA binds the TIFY motif of most JAZ repressors.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor. JAZ proteins act as transcriptional corepressors of MYC transcription factors and recruit TOPLESS via NINJA.

Proposed replacements: transcription corepressor binding

Summary: NINJA binds group-II TIFY proteins (PEAPOD1/2, TIFY8) through their TIFY motif.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor. PPD and TIFY8 are TIFY-domain transcriptional repressors that, like JAZ proteins, use NINJA to recruit TOPLESS.

Proposed replacements: transcription corepressor binding

Summary: NINJA binds group-II TIFY proteins (PEAPOD1/2, TIFY8) through their TIFY motif.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor. PPD and TIFY8 are TIFY-domain transcriptional repressors that, like JAZ proteins, use NINJA to recruit TOPLESS.

Proposed replacements: transcription corepressor binding

Summary: NINJA binds group-II TIFY proteins (PEAPOD1/2, TIFY8) through their TIFY motif.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor. PPD and TIFY8 are TIFY-domain transcriptional repressors that, like JAZ proteins, use NINJA to recruit TOPLESS.

Proposed replacements: transcription corepressor binding

Summary: NINJA binds the TIFY motif of most JAZ repressors.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor. JAZ proteins act as transcriptional corepressors of MYC transcription factors and recruit TOPLESS via NINJA.

Proposed replacements: transcription corepressor binding

Summary: NINJA binds the TIFY motif of most JAZ repressors.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor. JAZ proteins act as transcriptional corepressors of MYC transcription factors and recruit TOPLESS via NINJA.

Proposed replacements: transcription corepressor binding

Summary: NINJA binds TOPLESS and TPL-related corepressors through its EAR motif in domain A.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor (TPL/TPR are Groucho/Tup1-type corepressors).

Proposed replacements: transcription corepressor binding

Summary: NINJA binds the TIFY motif of most JAZ repressors.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor. JAZ proteins act as transcriptional corepressors of MYC transcription factors and recruit TOPLESS via NINJA.

Proposed replacements: transcription corepressor binding

Summary: NINJA binds group-II TIFY proteins (PEAPOD1/2, TIFY8) through their TIFY motif.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor. PPD and TIFY8 are TIFY-domain transcriptional repressors that, like JAZ proteins, use NINJA to recruit TOPLESS.

Proposed replacements: transcription corepressor binding

Summary: NINJA binds group-II TIFY proteins (PEAPOD1/2, TIFY8) through their TIFY motif.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor. PPD and TIFY8 are TIFY-domain transcriptional repressors that, like JAZ proteins, use NINJA to recruit TOPLESS.

Proposed replacements: transcription corepressor binding

Summary: NINJA binds the TIFY motif of most JAZ repressors.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor. JAZ proteins act as transcriptional corepressors of MYC transcription factors and recruit TOPLESS via NINJA.

Proposed replacements: transcription corepressor binding

Summary: NINJA binds the TIFY motif of most JAZ repressors.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor. JAZ proteins act as transcriptional corepressors of MYC transcription factors and recruit TOPLESS via NINJA.

Proposed replacements: transcription corepressor binding

Summary: NINJA binds TOPLESS and TPL-related corepressors through its EAR motif in domain A.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor (TPL/TPR are Groucho/Tup1-type corepressors).

Proposed replacements: transcription corepressor binding

Summary: NINJA binds the TIFY motif of most JAZ repressors.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor. JAZ proteins act as transcriptional corepressors of MYC transcription factors and recruit TOPLESS via NINJA.

Proposed replacements: transcription corepressor binding

Summary: NINJA binds the TIFY motif of most JAZ repressors.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor. JAZ proteins act as transcriptional corepressors of MYC transcription factors and recruit TOPLESS via NINJA.

Proposed replacements: transcription corepressor binding

Summary: NINJA binds the TIFY motif of most JAZ repressors.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor. JAZ proteins act as transcriptional corepressors of MYC transcription factors and recruit TOPLESS via NINJA.

Proposed replacements: transcription corepressor binding

Summary: NINJA binds the TIFY motif of most JAZ repressors.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor. JAZ proteins act as transcriptional corepressors of MYC transcription factors and recruit TOPLESS via NINJA.

Proposed replacements: transcription corepressor binding

Summary: NINJA binds the TIFY motif of most JAZ repressors.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor. JAZ proteins act as transcriptional corepressors of MYC transcription factors and recruit TOPLESS via NINJA.

Proposed replacements: transcription corepressor binding

Summary: NINJA binds the TIFY motif of most JAZ repressors.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor. JAZ proteins act as transcriptional corepressors of MYC transcription factors and recruit TOPLESS via NINJA.

Proposed replacements: transcription corepressor binding

Summary: NINJA binds the TIFY motif of most JAZ repressors.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor. JAZ proteins act as transcriptional corepressors of MYC transcription factors and recruit TOPLESS via NINJA.

Proposed replacements: transcription corepressor binding

Summary: NINJA interacts with PAT1H1, a topoisomerase II-associated protein homolog implicated in root stem cell niche maintenance.

Reason: Generic protein binding adds no functional information and the partner is not a characterized transcriptional regulator; removal does not imply the interaction is false. The root-meristem role is recorded in the notes rather than as an MF annotation.

Summary: NINJA interacts with PAT1H1, a topoisomerase II-associated protein homolog implicated in root stem cell niche maintenance.

Reason: Generic protein binding adds no functional information and the partner is not a characterized transcriptional regulator; removal does not imply the interaction is false. The root-meristem role is recorded in the notes rather than as an MF annotation.

Summary: NINJA binds group-II TIFY proteins (PEAPOD1/2, TIFY8) through their TIFY motif.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor. PPD and TIFY8 are TIFY-domain transcriptional repressors that, like JAZ proteins, use NINJA to recruit TOPLESS.

Proposed replacements: transcription corepressor binding

Summary: NINJA binds group-II TIFY proteins (PEAPOD1/2, TIFY8) through their TIFY motif.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor. PPD and TIFY8 are TIFY-domain transcriptional repressors that, like JAZ proteins, use NINJA to recruit TOPLESS.

Proposed replacements: transcription corepressor binding

Summary: NINJA binds group-II TIFY proteins (PEAPOD1/2, TIFY8) through their TIFY motif.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor. PPD and TIFY8 are TIFY-domain transcriptional repressors that, like JAZ proteins, use NINJA to recruit TOPLESS.

Proposed replacements: transcription corepressor binding

Summary: NINJA binds the TIFY motif of most JAZ repressors.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor. JAZ proteins act as transcriptional corepressors of MYC transcription factors and recruit TOPLESS via NINJA.

Proposed replacements: transcription corepressor binding

Summary: NINJA binds the TIFY motif of most JAZ repressors.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor. JAZ proteins act as transcriptional corepressors of MYC transcription factors and recruit TOPLESS via NINJA.

Proposed replacements: transcription corepressor binding

Summary: NINJA binds the TIFY motif of most JAZ repressors.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor. JAZ proteins act as transcriptional corepressors of MYC transcription factors and recruit TOPLESS via NINJA.

Proposed replacements: transcription corepressor binding

Summary: NINJA binds the TIFY motif of most JAZ repressors.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor. JAZ proteins act as transcriptional corepressors of MYC transcription factors and recruit TOPLESS via NINJA.

Proposed replacements: transcription corepressor binding

Summary: NINJA binds the TIFY motif of most JAZ repressors.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor. JAZ proteins act as transcriptional corepressors of MYC transcription factors and recruit TOPLESS via NINJA.

Proposed replacements: transcription corepressor binding

Summary: NINJA binds the TIFY motif of most JAZ repressors.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor. JAZ proteins act as transcriptional corepressors of MYC transcription factors and recruit TOPLESS via NINJA.

Proposed replacements: transcription corepressor binding

Summary: High-throughput hormone-network interaction between NINJA and the gibberellin receptor GID1A.

Reason: Abstract-only, large-scale yeast two-hybrid evidence; generic protein binding adds no functional information and the GID1A pairing has no supporting functional context. Removal does not imply the interaction is false.

Summary: NINJA binds the TIFY motif of most JAZ repressors.

Reason: Generic protein binding is uninformative; the functional meaning of this interaction is captured by binding to a transcriptional corepressor. JAZ proteins act as transcriptional corepressors of MYC transcription factors and recruit TOPLESS via NINJA.

Proposed replacements: transcription corepressor binding

Summary: NINJA-GFP is nuclear in Arabidopsis seedlings.

Reason: Nucleus is the site of NINJA corepressor-adaptor function; inferred annotations agree with direct evidence.

Summary: NINJA-GFP is nuclear in Arabidopsis seedlings.

Reason: Nucleus is the site of NINJA corepressor-adaptor function; inferred annotations agree with direct evidence.

Summary: BiFC shows NINJA-PPD2 complexes in nuclei.

Reason: Consistent with NINJA nuclear localization and transcriptional repressor function.

Summary: NINJA-GFP is nuclear in Arabidopsis seedlings.

Reason: Nucleus is the site of NINJA corepressor-adaptor function; inferred annotations agree with direct evidence.

Summary: NINJA-GFP is nuclear in Arabidopsis seedlings.

Reason: Nucleus is the site of NINJA corepressor-adaptor function; inferred annotations agree with direct evidence.

Summary: InterPro2GO assigns signal transduction from the NINJA/AFP family domain.

Reason: Uninformative parent term; NINJA's specific role is transcriptional repression within jasmonate signaling, captured by more specific annotations (GO:0009867, GO:0045892).

Summary: NINJA transcripts are induced by methyl jasmonate.

Reason: Expression response consistent with feedback in jasmonate signaling; NINJA also controls JA sensitivity, but the IEP itself is a non-core expression attribute.

Summary: Phylogenetic inference that NINJA family members act in jasmonate signaling.

Reason: Consistent with experimental NINJA overexpression and knockdown phenotypes (PMID:20360743).

Summary: NINJA overexpression reduces and knockdown enhances jasmonate responses.

Reason: NINJA is a direct component of the JAZ-NINJA-TPL repressor complex in jasmonate signaling, acting as a negative regulator.

Summary: Phylogenetic inference that NINJA/AFP proteins negatively regulate transcription.

Reason: Consistent with direct repression assays for NINJA (PMID:20360743).

Summary: NINJA represses reporter transcription in protoplasts, requiring its TPL-binding EAR motif.

Reason: Direct evidence for the core transcriptional repressor function.

Summary: ninja loss-of-function causes dome-shaped leaves resembling ppd mutants, via derepressed CYCD3;2.

Reason: A developmental role through the PPD2-NINJA repressor complex; genuine but not the jasmonate-pathway core.

Summary: NINJA represses transcription when tethered to DNA and bridges JAZ proteins to TOPLESS corepressors via its EAR motif.

Reason: GOA carries only generic protein binding and negative regulation of transcription for NINJA. The protoplast repression assays (EAR motif necessary and sufficient for repression) and the JAZ/TPL binding data show NINJA acts as a non-DNA-binding transcriptional corepressor that mediates repression by JAZ proteins, matching the definition of transcription corepressor activity.