Canonical nuclear auxin signaling in land plants

Canonical nuclear auxin signaling couples TIR1/AFB–Aux/IAA co-receptor assembly to regulated transcription by ARF proteins. Auxin enhances receptor–degron association, enabling SCF-dependent Aux/IAA turnover and reducing corepression of class-A ARFs. This circuit is represented by native Arabidopsis and Marchantia implementations within land plants; older algal ARF DNA-binding systems alone do not establish the complete circuit. Arabidopsis TIR1 also produces cAMP, and separation-of-function experiments show that substrate degradation alone does not guarantee transcriptional activation. The downstream cAMP effector remains unidentified, and MpTIR1 AC activity is untested. Marchantia class-B MpARF2 provides an additional active TOPLESS-recruiting repression and DNA-competition branch. Paralog combinations, expression domains and promoter/chromatin contexts determine output; neither all ARFs nor all Aux/IAAs share one regulatory behavior. Auxin synthesis/transport, rapid cytoplasmic or cell-surface pathways, noncanonical receptor routes and the downstream developmental programs are outside this boundary.

MODULE:auxin_nuclear_signalingCOMPLETECONCRETESignaling Pathwaymodules/auxin_nuclear_signaling.yaml
auxin-activated signaling pathwayGO:0009734
PMID:42590969
The canonical nuclear circuit must be distinguished from older ARF DNA-regulatory capacity.
algal ARFs are not connected to a canonical auxin response pathway
PMID:36529527
Native MpTIR1 binds the MpIAA DII-containing fragment auxin-dependently; DII mutation prevents recruitment.
The MpTIR1-3xFLAG proteins showed interactions with MpIAA only when auxin was added to the mixture
PMID:40044868
Matched ccvTIR1 ACm1/ACm3 lines retain degradation of full-length IAA6/IAA7/IAA8/IAA17 reporters.
comparable cvxIAA-induced degradation of all these Aux/IAAs in pTIR1::ccvTIR1, pTIR1::ccvTIR1ACm1 and pTIR1::ccvTIR1ACm3
PMID:40044868
The same catalytic mutants reduce or eliminate DR5 transcriptional reporter activation, separating turnover from sufficient transcriptional output.
cvxIAA-induced DR5::Luc activation was strongly reduced in pTIR1::ccvTIR1ACm1 and completely lost in the pTIR1::ccvTIR1ACm3 line

Exact gene-product selectors constrain functional claims; verified PANTHER subfamilies record classification without transferring activity to all members. Each native implementation requires receptor/adaptor, corepressor machinery and activator-ARF roles; the characterized TIR1 arm additionally requires its AC atom. AFB2 and Marchantia AC dependence remains unresolved, so their structural coverage is not a claim of AC-independent sufficiency. Feedback and MpARF2 modulation are optional contexts and cannot satisfy the circuit alone. No degradation-to-activation CAUSES edge is asserted. Generic SCF core, E1/E2, ubiquitin, proteasome, transcription machinery and ligand/cofactor supply are required boundary assumptions. MpTPL participation in canonical MpIAA repression includes conserved inference; engineered fusions and added-NLS promoter reporters are not native interaction/localization proofs. Current provider runs failed authentication/quota; manual primary-source research is documented. No bounded-index GO-CAM match was found for the 14 selected accessions. PR5076 overlaps earlier broad family additions; exact-member classification avoids its implied broad functional transfer. The required adenylate-cyclase activity in the assayed Arabidopsis TIR1 implementation rests on the 2025 AC-mutant transcriptional study (PMID:40044868); independent confirmation and the physiological significance of low purified catalytic rates remain open. The alternative AFB2 implementation does not inherit an unmeasured cyclase requirement.

26Nodes
16Parts
4Variant Sets
9Variants
19Annotons
13Connections

Derived QC

Recommended-field compliance

93.8% recommended fields populated
  • knowledge_gaps[0].provenance[0] · reference_section_type (0/1)
  • knowledge_gaps[1].provenance[0] · reference_section_type (0/1)
  • knowledge_gaps[2].provenance[0] · reference_section_type (0/1)

Module deep research

✗ none found

No MODULE:auxin_nuclear_signaling deep-research report alongside the module YAML.

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Function consistency and core coverage

19 gene-function check(s) reflected in core functions · 0 conflict(s) · 19 evidence or coverage gap(s) (38 comparison(s))

Retained noncore functions are reported separately; they do not require promotion to core functions. Support from representative genes does not establish conservation across the whole family. Missing reviews or identifiers leave a claim unverified.

AnnotonParticipantFunctionAssessment
tir1_receptor TIR1
UniProtKB:Q570C0
Gene 		auxin receptor activity
GO:0038198 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
tir1_adaptor TIR1
UniProtKB:Q570C0
Gene 		ubiquitin-like ligase-substrate adaptor activity
GO:1990756 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
tir1_adenylate_cyclase TIR1
UniProtKB:Q570C0
Gene 		adenylate cyclase activity
GO:0004016 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
afb2_receptor AFB2
UniProtKB:Q9LW29
Gene 		auxin receptor activity
GO:0038198 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
afb2_adaptor AFB2
UniProtKB:Q9LW29
Gene 		ubiquitin-like ligase-substrate adaptor activity
GO:1990756 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
iaa12_corepressor IAA12
UniProtKB:Q38830
Gene 		transcription corepressor activity
GO:0003714 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
iaa17_corepressor IAA17
UniProtKB:P93830
Gene 		transcription corepressor activity
GO:0003714 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
tpl_corepressor TPL
UniProtKB:Q94AI7
Gene 		transcription corepressor activity
GO:0003714 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
arf5_activator ARF5
UniProtKB:P93024
Gene 		DNA-binding transcription activator activity
GO:0001216 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
arf7_activator ARF7
UniProtKB:P93022
Gene 		DNA-binding transcription activator activity
GO:0001216 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
arf19_activator ARF19
UniProtKB:Q8RYC8
Gene 		DNA-binding transcription activator activity
GO:0001216 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
iaa19_feedback_corepressor IAA19
UniProtKB:O24409
Gene 		transcription corepressor activity
GO:0003714 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
mptir1_receptor MpTIR1
UniProtKB:A0A0K2QW32
Gene 		auxin receptor activity
GO:0038198 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
mptir1_adaptor MpTIR1
UniProtKB:A0A0K2QW32
Gene 		ubiquitin-like ligase-substrate adaptor activity
GO:1990756 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
mpiaa_corepressor MpIAA
UniProtKB:A0A0G3FNI9
Gene 		transcription corepressor activity
GO:0003714 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
mptpl_corepressor MpTPL
UniProtKB:A0A0G3FGV9
Gene 		transcription corepressor activity
GO:0003714 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
mparf1_activator MpARF1
UniProtKB:A0A0G3FLP1
Gene 		DNA-binding transcription activator activity
GO:0001216 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
mparf2_repressor MpARF2
UniProtKB:A0A0G3FH20
Gene 		DNA-binding transcription repressor activity
GO:0001217 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
mptpl_class_b_corepressor MpTPL
UniProtKB:A0A0G3FGV9
Gene 		transcription corepressor activity
GO:0003714 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
tir1_receptor TIR1 verified PANTHER classification
PANTHER:PTHR16134:SF66
Family 		auxin receptor activity
GO:0038198 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR16134:SF66.
tir1_adaptor TIR1 verified PANTHER classification
PANTHER:PTHR16134:SF66
Family 		ubiquitin-like ligase-substrate adaptor activity
GO:1990756 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR16134:SF66.
tir1_adenylate_cyclase TIR1 verified PANTHER classification
PANTHER:PTHR16134:SF66
Family 		adenylate cyclase activity
GO:0004016 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR16134:SF66.
afb2_receptor AFB2 verified PANTHER classification
PANTHER:PTHR16134:SF132
Family 		auxin receptor activity
GO:0038198 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR16134:SF132.
afb2_adaptor AFB2 verified PANTHER classification
PANTHER:PTHR16134:SF132
Family 		ubiquitin-like ligase-substrate adaptor activity
GO:1990756 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR16134:SF132.
iaa12_corepressor IAA12 verified PANTHER classification
PANTHER:PTHR31734:SF131
Family 		transcription corepressor activity
GO:0003714 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR31734:SF131.
iaa17_corepressor IAA17 verified PANTHER classification
PANTHER:PTHR31734:SF126
Family 		transcription corepressor activity
GO:0003714 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR31734:SF126.
tpl_corepressor TPL verified PANTHER classification
PANTHER:PTHR44083:SF27
Family 		transcription corepressor activity
GO:0003714 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR44083:SF27.
arf5_activator ARF5 verified PANTHER classification
PANTHER:PTHR31384:SF10
Family 		DNA-binding transcription activator activity
GO:0001216 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR31384:SF10.
arf7_activator ARF7 verified PANTHER classification
PANTHER:PTHR31384:SF93
Family 		DNA-binding transcription activator activity
GO:0001216 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR31384:SF93.
arf19_activator ARF19 verified PANTHER classification
PANTHER:PTHR31384:SF21
Family 		DNA-binding transcription activator activity
GO:0001216 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR31384:SF21.
iaa19_feedback_corepressor IAA19 verified PANTHER classification
PANTHER:PTHR31734:SF121
Family 		transcription corepressor activity
GO:0003714 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR31734:SF121.
mptir1_receptor MpTIR1 verified PANTHER classification
PANTHER:PTHR16134:SF148
Family 		auxin receptor activity
GO:0038198 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR16134:SF148.
mptir1_adaptor MpTIR1 verified PANTHER classification
PANTHER:PTHR16134:SF148
Family 		ubiquitin-like ligase-substrate adaptor activity
GO:1990756 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR16134:SF148.
mpiaa_corepressor MpIAA verified PANTHER classification
PANTHER:PTHR31734:SF28
Family 		transcription corepressor activity
GO:0003714 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR31734:SF28.
mptpl_corepressor MpTPL verified PANTHER classification
PANTHER:PTHR44083:SF45
Family 		transcription corepressor activity
GO:0003714 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR44083:SF45.
mparf1_activator MpARF1 verified PANTHER classification
PANTHER:PTHR31384:SF115
Family 		DNA-binding transcription activator activity
GO:0001216 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR31384:SF115.
mparf2_repressor MpARF2 verified PANTHER classification
PANTHER:PTHR31384:SF1
Family 		DNA-binding transcription repressor activity
GO:0001217 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR31384:SF1.
mptpl_class_b_corepressor MpTPL verified PANTHER classification
PANTHER:PTHR44083:SF45
Family 		transcription corepressor activity
GO:0003714 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR44083:SF45.

Feedback loops (advisory, prose-driven: a regulator counts as "feedback" when its own description says so)

✓ every negative regulator described as feedback has an upstream edge closing the loop.

  • aux_iaa_degradation ⊣ aux_iaa_tpl_repression [closed]
    aux_iaa_degradation is regulated by auxin_perception: feedback loop closed
  • aux_iaa_tpl_repression ⊣ arf_activation [input]
    aux_iaa_tpl_repression is a negative regulator with no upstream edge (not described as feedback)
  • iaa19_feedback_corepressor ⊣ arf7_activator [closed]
    iaa19_feedback_corepressor is regulated by arf7_activator: feedback loop closed
  • at_afb2_adaptor ⊣ aux_iaa_tpl_repression [closed]
    at_afb2_adaptor is regulated by at_afb2_perception: feedback loop closed
  • mp_aux_iaa_degradation ⊣ mp_aux_iaa_repression [closed]
    mp_aux_iaa_degradation is regulated by mp_auxin_perception: feedback loop closed
  • mp_aux_iaa_repression ⊣ mp_arf_activation [input]
    mp_aux_iaa_repression is a negative regulator with no upstream edge (not described as feedback)
  • mp_class_b_repression ⊣ mp_arf_activation [input]
    mp_class_b_repression is a negative regulator with no upstream edge (not described as feedback)

Gene-review completeness (14/14 grounded genes reviewed)

12 complete review(s) · 3 with deep research · 0 missing review · 11 reviewed but lacking deep research

Gene Review Complete Deep research
AFB2 Q9LW29 ✓ 16/17 ✗
ARF19 Q8RYC8 ✓ ✓ ✓
ARF5 P93024 ✓ ✓ ✓
ARF7 P93022 ✓ ✓ ✗
IAA12 Q38830 ✓ ✓ ✗
IAA17 P93830 ✓ ✓ ✗
IAA19 O24409 ✓ ✓ ✗
MpARF1 A0A0G3FLP1 ✓ ✓ ✗
MpARF2 A0A0G3FH20 ✓ ✓ ✗
MpIAA A0A0G3FNI9 ✓ ✓ ✗
MpTIR1 A0A0K2QW32 ✓ ✓ ✗
MpTPL A0A0G3FGV9 ✓ ✓ ✗
TIR1 Q570C0 ✓ ✓ ✓
TPL Q94AI7 ✓ 123/124 ✗

Details

Context
land plantsNCBITaxon:3193
nucleusGO:0005634

The nucleus scopes the transcriptional circuit, not exclusive localization of every component; AFB2 has a cytoplasmic pool and MpTPL localization is not established by an added-NLS reporter.

Land-plant canonical nuclear auxin circuitSignaling Pathwayauxin_nuclear_signaling
auxin-activated signaling pathwayGO:0009734
Context
land plantsNCBITaxon:3193
nucleusGO:0005634

The nucleus scopes the transcriptional circuit, not exclusive localization of every component; AFB2 has a cytoplasmic pool and MpTPL localization is not established by an added-NLS reporter.

Variant set: Complete native implementations by taxon / experimentally grounded circuit (One Or More)

Presence of an alternative establishes a supported role, not unique necessity or equivalence of every interaction pair.

Arabidopsis native nuclear auxin circuitRegulatory Steparabidopsis_native

Required receptor-specific mechanism, Aux/IAA–TOPLESS repression machinery and activator-ARF output. TIR1’s characterized mechanism additionally requires its AC activity; the AFB2 alternative records established roles with explicitly unresolved AC dependence. Structural coverage of the AFB2 alternative is not evidence of AC-independent sufficiency.

Context
Arabidopsis thalianaNCBITaxon:3702

Connections

TIR1 co-receptor assembly promotes recruitment of Aux/IAA to SCF and turnover; an intact ubiquitin/proteasome system is assumed.
PMID:17410169
TIR1 structural auxin/substrate recognition supports the molecular-glue mechanism.
auxin enhances the TIR1-substrate interactions by acting as a 'molecular glue'
PMID:11713520
Auxin promotes SCF(TIR1) recognition and degradation of IAA7/IAA17 substrates.
auxin stimulates binding of SCF(TIR1) to the AUX/IAA proteins, and their degradation
Removal of Aux/IAA reduces its repressive contribution. This edge does not assert that removal alone suffices for ARF activation.
PMID:11713520
Auxin promotes SCF(TIR1) recognition and degradation of IAA7/IAA17 substrates.
auxin stimulates binding of SCF(TIR1) to the AUX/IAA proteins, and their degradation
PMID:14742873
Aux/IAA domain I supplies active transcriptional repression, including IAA17 constructs.
domain I in Aux/IAA proteins is an active repression domain that is transferable and dominant over activation domains
aux_iaa_tpl_repression -> arf_activation Negatively Regulates
Aux/IAA–ARF binding and recruited TPL restrain activator output; the exact pairs and tissues remain source-specific.
PMID:18258861
Direct IAA12–TPL interaction and genetic evidence support repression of the ARF5-dependent embryonic program.
We show that TOPLESS (TPL) can physically interact with IAA12/BODENLOS (IAA12/BDL)
PMID:24706860
ARF7–IAA17 interactions are disrupted by PB1 interface mutations.
Mutation of interface residues in the ARF7 PB1 domain yields monomeric protein and abolishes interaction with both itself and IAA17
tir1_receptor -> tir1_camp_branch Positively Regulates
Assembly of the TIR1–auxin–Aux/IAA co-receptor enhances TIR1 AC activity; this does not ascribe AC to AFB2.
file:publications/url_https___pure.coventry.ac.uk_ws_portalfiles_portal_60931587_Post_Print.pdf.md
TIR1-specific purified assay with auxin and IAA7/IAA17.
significant increase in TIR1 AC activity was observed in the presence of IAA together with IAA7 or IAA17
tir1_camp_branch -> arf_activation Positively Regulates
TIR1-produced cAMP supports transcriptional competence in tested Arabidopsis responses. This is an indirect causal link with unidentified effector; engineered local-AC bypass is not a native cAMP–ARF binding measurement.
PMID:40044868
Matched ccvTIR1 ACm1/ACm3 lines retain degradation of full-length IAA6/IAA7/IAA8/IAA17 reporters.
comparable cvxIAA-induced degradation of all these Aux/IAAs in pTIR1::ccvTIR1, pTIR1::ccvTIR1ACm1 and pTIR1::ccvTIR1ACm3
PMID:40044868
The same catalytic mutants reduce or eliminate DR5 transcriptional reporter activation, separating turnover from sufficient transcriptional output.
cvxIAA-induced DR5::Luc activation was strongly reduced in pTIR1::ccvTIR1ACm1 and completely lost in the pTIR1::ccvTIR1ACm3 line
ARF7 promotes IAA19 expression, replenishing a transcriptional repressor in a documented feedback context.
PMID:14729917
ARF7-dependent IAA19 induction supplies a specific negative-feedback example; this quantitative result is not generalized to all Aux/IAAs.
auxin inducibility of MSG2/IAA19 gene expression is reduced by 65% in nph4/arf7
IAA19 binds and represses ARF7-dependent output; the loop is conditional on both components being expressed.
PMID:14729917
Direct interaction and native genetic evidence support a specific feedback loop.
These results suggest that MSG2/IAA19 and NPH4/ARF7 may constitute a negative feedback loop
Auxin-dependent AFB2–Aux/IAA recognition supports SCF substrate recruitment; no AFB2 AC measurement is inferred.
PMID:15992545
AFB family receptors bind BDL and promote its turnover in the tested genetic context.
all TIR1/AFB proteins interact with BDL, and BDL is stabilized in triple mutant plants
at_afb2_adaptor -> aux_iaa_tpl_repression Negatively Regulates
AFB2-associated Aux/IAA turnover limits corepression, without demonstrating that this alone is sufficient for transcription.
PMID:15992545
AFB family receptors bind BDL and promote its turnover in the tested genetic context.
all TIR1/AFB proteins interact with BDL, and BDL is stabilized in triple mutant plants
Part 1: Receptor-specific input and transduction mechanism
Arabidopsis receptor-specific mechanism contextsRegulatory Stepat_receptor_implementation

Receptor roles are coupled within a variant to prevent a TIR1 perception route from dropping its experimentally required AC contribution or borrowing a different receptor’s adaptor atom.

Variant set: Receptor-specific evidence boundary by tested receptor mechanism / resolved versus unresolved AC contribution (One Or More)
TIR1 mechanism with required cAMP contributionSignaling Pathwayat_tir1_transcription_mechanism

The characterized TIR1 implementation requires receptor recognition, SCF substrate recruitment and demonstrated AC activity. Removing the AC atom fails this implementation even though substrate turnover remains biochemically possible. AC-mutant DR5 and full-length Aux/IAA assays distinguish these outcomes.

Part 1: Auxin recognition
TIR1 auxin co-receptor assemblyRegulatory Stepauxin_perception

TIR1 structural and biochemical co-receptor evidence.

Annotons

TIR1: auxin receptor activity
tir1_receptor
Participant: Gene Product: TIR1
Gene Product:
TIR1UniProtKB:Q570C0
Family:
TIR1 verified PANTHER classificationPANTHER:PTHR16134:SF66 Classification of the exact selected protein; does not select every member for this activity.
Representative Members: TIR1UniProtKB:Q570C0
Taxon:
Arabidopsis thalianaNCBITaxon:3702
The exact gene product is the functional selector. The family descriptor records verified membership only.

Function

auxin receptor activityGO:0038198

Locations

nucleusGO:0005634

Auxin stabilizes the receptor–Aux/IAA interface; InsP6 is an integral structural cofactor, not a separately modeled obligatory biosynthetic supply step.

Part 2: SCF substrate recruitment
TIR1 SCF substrate recruitment and Aux/IAA turnoverRegulatory Stepaux_iaa_degradation

Auxin-dependent recruitment of substrates to SCF.

Annotons

TIR1: ubiquitin-like ligase-substrate adaptor activity
tir1_adaptor
Participant: Gene Product: TIR1
Gene Product:
TIR1UniProtKB:Q570C0
Family:
TIR1 verified PANTHER classificationPANTHER:PTHR16134:SF66 Classification of the exact selected protein; does not select every member for this activity.
Representative Members: TIR1UniProtKB:Q570C0
Taxon:
Arabidopsis thalianaNCBITaxon:3702
The exact gene product is the functional selector. The family descriptor records verified membership only.

Function

ubiquitin-like ligase-substrate adaptor activityGO:1990756

Locations

nucleusGO:0005634

Presents the Aux/IAA degron to SCF for ubiquitination and subsequent proteasomal degradation.

Part 3: Demonstrated cAMP contribution to transcription
TIR1-generated cAMP contributionRegulatory Steptir1_camp_branch

TIR1 catalyzes ATP-to-cAMP conversion. Auxin plus Aux/IAA can enhance this activity. AC-deficient mutants retain substrate degradation while impairing transcription. AFB2 and MpTIR1 catalytic capacity is not established by these studies; an untested family member is neither a positive nor a negative assay result.

Context
Arabidopsis thalianaNCBITaxon:3702
TIR1-dependent transcriptional auxin-response experiments

Annotons

TIR1: adenylate cyclase activity
tir1_adenylate_cyclase
Participant: Gene Product: TIR1
Gene Product:
TIR1UniProtKB:Q570C0
Family:
TIR1 verified PANTHER classificationPANTHER:PTHR16134:SF66 Classification of the exact selected protein; does not select every member for this activity.
Representative Members: TIR1UniProtKB:Q570C0
Taxon:
Arabidopsis thalianaNCBITaxon:3702
The exact gene product is the functional selector. The family descriptor records verified membership only.

Function

adenylate cyclase activityGO:0004016

Locations

nucleusGO:0005634

Source-specific Arabidopsis cAMP output. The observed low purified rate is not equated with native flux, and AFB5 metal preference is not transferred to TIR1.

AFB2 established receptor/adaptor contribution; AC dependence unresolvedSignaling Pathwayat_afb2_established_mechanism

Native receptor/adaptor and auxin-response evidence establish these AFB2 contributions. Direct AC catalysis or an AC-independent sufficient transcription mechanism has not been demonstrated for AFB2; lack of an AC atom records an unknown, not biochemical dispensability. The shared output machinery represents observed signaling involvement, not a reconstituted sufficient AFB2-only system.

Part 1: Auxin recognition
AFB2 perceptionRegulatory Stepat_afb2_perception

Native genetics and direct Aux/IAA interaction support AFB2 receptor function.

Annotons

AFB2: auxin receptor activity
afb2_receptor
Participant: Gene Product: AFB2
Gene Product:
AFB2UniProtKB:Q9LW29
Family:
AFB2 verified PANTHER classificationPANTHER:PTHR16134:SF132 Classification of the exact selected protein; does not select every member for this activity.
Representative Members: AFB2UniProtKB:Q9LW29
Taxon:
Arabidopsis thalianaNCBITaxon:3702
The exact gene product is the functional selector. The family descriptor records verified membership only.

Function

auxin receptor activityGO:0038198

Locations

nucleusGO:0005634

Auxin-dependent Aux/IAA recognition; AFB2 also has an observed cytoplasmic pool, but this leaf selects its nuclear signaling contribution.

Part 2: SCF substrate recruitment
AFB2 SCF adaptorRegulatory Stepat_afb2_adaptor

Auxin-dependent recruitment of substrates to SCF.

Annotons

AFB2: ubiquitin-like ligase-substrate adaptor activity
afb2_adaptor
Participant: Gene Product: AFB2
Gene Product:
AFB2UniProtKB:Q9LW29
Family:
AFB2 verified PANTHER classificationPANTHER:PTHR16134:SF132 Classification of the exact selected protein; does not select every member for this activity.
Representative Members: AFB2UniProtKB:Q9LW29
Taxon:
Arabidopsis thalianaNCBITaxon:3702
The exact gene product is the functional selector. The family descriptor records verified membership only.

Function

ubiquitin-like ligase-substrate adaptor activityGO:1990756

Locations

nucleusGO:0005634

Presents the Aux/IAA degron to SCF for ubiquitination and subsequent proteasomal degradation.

Part 2: Repression machinery
Arabidopsis Aux/IAA–TOPLESS repressionRegulatory Stepaux_iaa_tpl_repression

At low effective auxin signaling, Aux/IAA repressors restrain activator ARFs. Direct pairwise evidence is strongest for IAA12/TPL/ARF5 and IAA17/ARF7; specific promoter/chromatin configurations differ.

Part: Aux/IAA corepressor
Canonical Aux/IAA repressionRegulatory Stepat_aux_iaa_repressor

IAA12 and IAA17 illustrate canonical repression. Their transcription-factor and receptor interactions are source- and pair-specific; this choice does not assert every possible receptor/ARF pairing in every tissue.

Variant set: Canonical repressor exemplars by reviewed paralog / expressed biochemical implementation (One Or More)

Presence of an alternative establishes a supported role, not unique necessity or equivalence of every interaction pair.

IAA12 corepressorRegulatory Stepat_iaa12_repression

Aux/IAA repression through interaction with ARFs and repression machinery.

Annotons

IAA12: transcription corepressor activity
iaa12_corepressor
Participant: Gene Product: IAA12
Gene Product:
IAA12UniProtKB:Q38830
Family:
IAA12 verified PANTHER classificationPANTHER:PTHR31734:SF131 Classification of the exact selected protein; does not select every member for this activity.
Representative Members: IAA12UniProtKB:Q38830
Taxon:
Arabidopsis thalianaNCBITaxon:3702
The exact gene product is the functional selector. The family descriptor records verified membership only.

Function

transcription corepressor activityGO:0003714

Locations

nucleusGO:0005634

IAA12–ARF5 and IAA17–ARF7 provide distinct direct interaction examples; the role is active corepression.

IAA17 corepressorRegulatory Stepat_iaa17_repression

Aux/IAA repression through interaction with ARFs and repression machinery.

Annotons

IAA17: transcription corepressor activity
iaa17_corepressor
Participant: Gene Product: IAA17
Gene Product:
IAA17UniProtKB:P93830
Family:
IAA17 verified PANTHER classificationPANTHER:PTHR31734:SF126 Classification of the exact selected protein; does not select every member for this activity.
Representative Members: IAA17UniProtKB:P93830
Taxon:
Arabidopsis thalianaNCBITaxon:3702
The exact gene product is the functional selector. The family descriptor records verified membership only.

Function

transcription corepressor activityGO:0003714

Locations

nucleusGO:0005634

IAA12–ARF5 and IAA17–ARF7 provide distinct direct interaction examples; the role is active corepression.

Part: TOPLESS repression machinery
TOPLESS corepressionRegulatory Stepat_tpl_repression

TPL is recruited by repression motifs; Mediator and chromatin effects depend on assay and context.

Annotons

TPL: transcription corepressor activity
tpl_corepressor
Participant: Gene Product: TPL
Gene Product:
TPLUniProtKB:Q94AI7
Family:
TPL verified PANTHER classificationPANTHER:PTHR44083:SF27 Classification of the exact selected protein; does not select every member for this activity.
Representative Members: TPLUniProtKB:Q94AI7
Taxon:
Arabidopsis thalianaNCBITaxon:3702
The exact gene product is the functional selector. The family descriptor records verified membership only.

Function

transcription corepressor activityGO:0003714

Locations

nucleusGO:0005634

IAA12 EAR-dependent recruitment directly supports the auxin role. Mediator engagement was tested in synthetic yeast and plant systems; no universal obligate HDAC/Mediator stoichiometry is imposed.

Part 3: ARF transcriptional output
Arabidopsis activator-ARF transcriptional outputRegulatory Steparf_activation

Loss of Aux/IAA repression can permit class-A ARF activity; it is not asserted to be sufficient for activation. TIR1 cAMP separation experiments reveal an additional requirement in the tested contexts, and coactivators/chromatin contribute. Repressor/noncanonical ARFs are not activator alternatives.

Variant set: Native activator ARF contexts by expressed ARF / developmental context (One Or More)

Presence of an alternative establishes a supported role, not unique necessity or equivalence of every interaction pair.

ARF5 transcriptional outputRegulatory Stepat_arf5_output

A context-selected activator ARF; class-A behavior is not assigned to all ARFs.

Annotons

ARF5: DNA-binding transcription activator activity
arf5_activator
Participant: Gene Product: ARF5
Gene Product:
ARF5UniProtKB:P93024
Family:
ARF5 verified PANTHER classificationPANTHER:PTHR31384:SF10 Classification of the exact selected protein; does not select every member for this activity.
Representative Members: ARF5UniProtKB:P93024
Taxon:
Arabidopsis thalianaNCBITaxon:3702
The exact gene product is the functional selector. The family descriptor records verified membership only.

Function

DNA-binding transcription activator activityGO:0001216

Locations

nucleusGO:0005634

Binds auxin-response DNA elements and promotes tested transcriptional outputs. AuxRE sequence, spacing and chromatin context matter; TGTCTC is an example rather than the only site.

ARF7 transcriptional outputRegulatory Stepat_arf7_output

A context-selected activator ARF; class-A behavior is not assigned to all ARFs.

Annotons

ARF7: DNA-binding transcription activator activity
arf7_activator
Participant: Gene Product: ARF7
Gene Product:
ARF7UniProtKB:P93022
Family:
ARF7 verified PANTHER classificationPANTHER:PTHR31384:SF93 Classification of the exact selected protein; does not select every member for this activity.
Representative Members: ARF7UniProtKB:P93022
Taxon:
Arabidopsis thalianaNCBITaxon:3702
The exact gene product is the functional selector. The family descriptor records verified membership only.

Function

DNA-binding transcription activator activityGO:0001216

Locations

nucleusGO:0005634

Binds auxin-response DNA elements and promotes tested transcriptional outputs. AuxRE sequence, spacing and chromatin context matter; TGTCTC is an example rather than the only site.

ARF19 transcriptional outputRegulatory Stepat_arf19_output

A context-selected activator ARF; class-A behavior is not assigned to all ARFs.

Annotons

ARF19: DNA-binding transcription activator activity
arf19_activator
Participant: Gene Product: ARF19
Gene Product:
ARF19UniProtKB:Q8RYC8
Family:
ARF19 verified PANTHER classificationPANTHER:PTHR31384:SF21 Classification of the exact selected protein; does not select every member for this activity.
Representative Members: ARF19UniProtKB:Q8RYC8
Taxon:
Arabidopsis thalianaNCBITaxon:3702
The exact gene product is the functional selector. The family descriptor records verified membership only.

Function

DNA-binding transcription activator activityGO:0001216

Locations

nucleusGO:0005634

Binds auxin-response DNA elements and promotes tested transcriptional outputs. AuxRE sequence, spacing and chromatin context matter; TGTCTC is an example rather than the only site.

Part 4: Specific ARF7–IAA19 feedback (optional)
ARF7–IAA19 feedback contextRegulatory Stepiaa19_feedback

ARF7-dependent induction replenishes a repressor that directly binds ARF7. The 65% induction reduction is specific to the tested nph4/arf7 context.

Annotons

IAA19: transcription corepressor activity
iaa19_feedback_corepressor
Participant: Gene Product: IAA19
Gene Product:
IAA19UniProtKB:O24409
Family:
IAA19 verified PANTHER classificationPANTHER:PTHR31734:SF121 Classification of the exact selected protein; does not select every member for this activity.
Representative Members: IAA19UniProtKB:O24409
Taxon:
Arabidopsis thalianaNCBITaxon:3702
The exact gene product is the functional selector. The family descriptor records verified membership only.

Function

transcription corepressor activityGO:0003714

Locations

nucleusGO:0005634

IAA19 binds ARF7 and supplies a demonstrated feedback example; it is not a mandatory part of every represented response.

Marchantia native nuclear auxin circuitRegulatory Stepmarchantia_native

Native receptor, repressor and class-A output evidence supplies a complete comparative implementation, with an additional class-B repression context. Knockout loss of normal organogenesis is distinguished from viable cell-mass survival. cAMP activity/dependence is untested for MpTIR1.

Context
Marchantia polymorphaNCBITaxon:3197

Connections

Auxin-dependent MpTIR1–MpIAA binding promotes substrate turnover; DII mutations prevent recruitment and receptor loss stabilizes the reporter.
PMID:36529527
Native MpTIR1 binds the MpIAA DII-containing fragment auxin-dependently; DII mutation prevents recruitment.
The MpTIR1-3xFLAG proteins showed interactions with MpIAA only when auxin was added to the mixture
PMID:36529527
Conditional native MpTIR1 knockout stabilizes the MpIAA DII reporter (Fig2C/D); SCF/proteasome assignment incorporates conserved mechanism rather than a native purified ligase assay.
Turnover limits canonical MpIAA repression; stabilized MpIAA inhibits native auxin-responsive expression. No claim of universally sufficient activation follows.
PMID:36529527
Conditional native MpTIR1 knockout stabilizes the MpIAA DII reporter (Fig2C/D); SCF/proteasome assignment incorporates conserved mechanism rather than a native purified ligase assay.
PMID:26020919
Stabilized MpIAA-GR represses an auxin-responsive reporter in native Marchantia; the 825-aa construct corroborates the same-locus 828-aa KP877968 exemplar.
plants completely repressed auxin-dependent expression of the GUS reporter gene
mp_aux_iaa_repression -> mp_arf_activation Negatively Regulates
MpIAA restrains the auxin-responsive class-A output; same-locus native mutants and interaction constructs support this assignment, without asserting every ARF is equally auxin gated.
PMID:26020919
Stabilized MpIAA-GR represses an auxin-responsive reporter in native Marchantia; the 825-aa construct corroborates the same-locus 828-aa KP877968 exemplar.
plants completely repressed auxin-dependent expression of the GUS reporter gene
file:publications/url_https___edepot.wur.nl_523089.md
Native functional comparisons and domain swaps distinguish class-A MpARF1 activation from class-B MpARF2 repression.
while MpARF1 activates transcription, MpARF2 and MpARF3 recruit MpTPL to repress transcription
mp_class_b_repression -> mp_arf_activation Negatively Regulates
MpARF2/TPL active repression and shared-site competition counteract class-A target output; this is not evidence that MpARF2 directly inhibits MpARF1 protein or activates its targets.
file:publications/url_https___edepot.wur.nl_523089.md
Full MpARF2 recruits MpTPL through its LFG motif in Arabidopsis-protoplast FRET–FLIM; native induced MpARF2 represses target transcripts. This is active repression as well as DNA competition.
showed a clear interaction with MpTPL
file:publications/url_https___edepot.wur.nl_523089.md
Native functional comparisons and domain swaps distinguish class-A MpARF1 activation from class-B MpARF2 repression.
while MpARF1 activates transcription, MpARF2 and MpARF3 recruit MpTPL to repress transcription
Part 1: Auxin recognition
Marchantia auxin co-receptor assemblyRegulatory Stepmp_auxin_perception

Native MpTIR1 recruitment of MpIAA DII is auxin dependent.

Annotons

MpTIR1: auxin receptor activity
mptir1_receptor
Participant: Gene Product: MpTIR1
Gene Product:
MpTIR1UniProtKB:A0A0K2QW32
Family:
MpTIR1 verified PANTHER classificationPANTHER:PTHR16134:SF148 Classification of the exact selected protein; does not select every member for this activity.
Representative Members: MpTIR1UniProtKB:A0A0K2QW32
Taxon:
Marchantia polymorphaNCBITaxon:3197
The exact gene product is the functional selector. The family descriptor records verified membership only.

Function

auxin receptor activityGO:0038198

Locations

nucleusGO:0005634

Plant-expressed MpTIR1 with recombinant MpIAA C-terminal fragments provides direct co-receptor evidence; functional fusion localization is reported as nucleus-like regions in sporelings.

Part 2: Substrate recruitment and turnover
Marchantia MpIAA turnoverRegulatory Stepmp_aux_iaa_degradation

Conditional receptor loss stabilizes the native DII reporter; conserved SCF architecture connects recruitment to proteolysis.

Annotons

MpTIR1: ubiquitin-like ligase-substrate adaptor activity
mptir1_adaptor
Participant: Gene Product: MpTIR1
Gene Product:
MpTIR1UniProtKB:A0A0K2QW32
Family:
MpTIR1 verified PANTHER classificationPANTHER:PTHR16134:SF148 Classification of the exact selected protein; does not select every member for this activity.
Representative Members: MpTIR1UniProtKB:A0A0K2QW32
Taxon:
Marchantia polymorphaNCBITaxon:3197
The exact gene product is the functional selector. The family descriptor records verified membership only.

Function

ubiquitin-like ligase-substrate adaptor activityGO:1990756

Locations

nucleusGO:0005634

Substrate-adaptor activity is corroborated directly; complete native SCF purification and ubiquitin-transfer reconstitution were not performed in the cited study.

Part 3: Canonical repression machinery
Marchantia Aux/IAA corepressionRegulatory Stepmp_aux_iaa_repression

Native MpIAA-dependent repression is established. MpTPL is a conserved repression component; forced MpTPL–MpIAA fusions demonstrate imposed repression, not an independently measured native binary recruitment interaction.

Annotons

MpIAA: transcription corepressor activity
mpiaa_corepressor
Participant: Gene Product: MpIAA
Gene Product:
MpIAAUniProtKB:A0A0G3FNI9
Family:
MpIAA verified PANTHER classificationPANTHER:PTHR31734:SF28 Classification of the exact selected protein; does not select every member for this activity.
Representative Members: MpIAAUniProtKB:A0A0G3FNI9
Taxon:
Marchantia polymorphaNCBITaxon:3197
The exact gene product is the functional selector. The family descriptor records verified membership only.

Function

transcription corepressor activityGO:0003714

Locations

nucleusGO:0005634

828-aa KP877968 exemplar; independent 825-aa same-locus constructs corroborate native repression without being treated as identical sequences.

MpTPL: transcription corepressor activity
mptpl_corepressor
Participant: Gene Product: MpTPL
Gene Product:
MpTPLUniProtKB:A0A0G3FGV9
Family:
MpTPL verified PANTHER classificationPANTHER:PTHR44083:SF45 Classification of the exact selected protein; does not select every member for this activity.
Representative Members: MpTPLUniProtKB:A0A0G3FGV9
Taxon:
Marchantia polymorphaNCBITaxon:3197
The exact gene product is the functional selector. The family descriptor records verified membership only.

Function

transcription corepressor activityGO:0003714

Native-circuit TPL contribution is a conserved mechanistic inference supported by repression constructs. Direct MpARF2–MpTPL interaction is separately documented in heterologous cells; promoter-NLS reporters do not measure native MpTPL localization.

Part 4: Class-A transcriptional output
Marchantia class-A MpARF1 outputRegulatory Stepmp_arf_activation

Native MpARF1 contributes to auxin-dependent transcription. DBD swaps show some shared DNA recognition with MpARF2, but do not convert the native class-B protein into an activator.

Annotons

MpARF1: DNA-binding transcription activator activity
mparf1_activator
Participant: Gene Product: MpARF1
Gene Product:
MpARF1UniProtKB:A0A0G3FLP1
Family:
MpARF1 verified PANTHER classificationPANTHER:PTHR31384:SF115 Classification of the exact selected protein; does not select every member for this activity.
Representative Members: MpARF1UniProtKB:A0A0G3FLP1
Taxon:
Marchantia polymorphaNCBITaxon:3197
The exact gene product is the functional selector. The family descriptor records verified membership only.

Function

DNA-binding transcription activator activityGO:0001216

Locations

nucleusGO:0005634

Full-length class-A activator. Native mutant transcriptomics and domain-interface tests support the output; a short isolated peptide can repress without overturning the full protein’s principal activity.

Part 5: Class-B output modulation (optional)
Marchantia class-B active repression and competitionRegulatory Stepmp_class_b_repression

MpARF2 actively recruits MpTPL through LFG and can compete with MpARF1 at shared DNA sites. This branch modulates output independently of the canonical MpIAA degradation gate; it is not an interchangeable activator.

Annotons

MpARF2: DNA-binding transcription repressor activity
mparf2_repressor
Participant: Gene Product: MpARF2
Gene Product:
MpARF2UniProtKB:A0A0G3FH20
Family:
MpARF2 verified PANTHER classificationPANTHER:PTHR31384:SF1 Classification of the exact selected protein; does not select every member for this activity.
Representative Members: MpARF2UniProtKB:A0A0G3FH20
Taxon:
Marchantia polymorphaNCBITaxon:3197
The exact gene product is the functional selector. The family descriptor records verified membership only.

Function

DNA-binding transcription repressor activityGO:0001217

Locations

nucleusGO:0005634

Full MpARF2–MpTPL interaction was measured by FRET–FLIM in Arabidopsis protoplasts; induced repression and conditional-loss phenotypes were tested in native Marchantia. Short-peptide tobacco assays and DBD chimeras are distinct evidence.

MpTPL: transcription corepressor activity
mptpl_class_b_corepressor
Participant: Gene Product: MpTPL
Gene Product:
MpTPLUniProtKB:A0A0G3FGV9
Family:
MpTPL verified PANTHER classificationPANTHER:PTHR44083:SF45 Classification of the exact selected protein; does not select every member for this activity.
Representative Members: MpTPLUniProtKB:A0A0G3FGV9
Taxon:
Marchantia polymorphaNCBITaxon:3197
The exact gene product is the functional selector. The family descriptor records verified membership only.

Function

transcription corepressor activityGO:0003714

LFG-dependent corepressor recruitment by MpARF2; inferred nuclear role is not supported by the added-NLS promoter reporter.