Bacterial iad-type aerobic indole-3-acetic acid catabolism

A conserved rhizosphere bacterial pathway module mediating aerobic uptake and catabolism of the plant hormone indole-3-acetic acid (IAA) via the iad gene cluster. The module comprises the MarR-family IAA-sensing transcriptional repressor IadR, the high-affinity periplasmic subcluster B-III ABC transporter solute-binding protein IadK2 (paired with its non-IAA-binding paralog IadK3), the Class IA NADH:ferredoxin oxidoreductase component IadC, the heterohexameric Rieske non-heme iron aromatic-ring-hydroxylating dioxygenase complex IadD/IadE that catalyzes the initial oxidative conversion of IAA into biologically inactive 2-oxindole-3-acetic acid (oxIAA), and the downstream cytoplasmic enzymes—including the heterodimeric TPP/[4Fe-4S]-dependent 2-oxoacid:ferredoxin oxidoreductase complex IadA/IadB and the putative cyclic-amide amidohydrolase / isatin hydrolase IadI (KynB2)—that participate in processing oxidized indole intermediates through dioxindole-3-acetic acid, dioxindole, isatin, and isatinic acid to anthranilic acid, thereby buffering rhizosphere auxin levels and preventing root growth inhibition.

MODULE:bacterial_iad_auxin_catabolismDRAFTMetabolic Pathwaymodules/bacterial_iad_auxin_catabolism.yaml
indoleacetic acid catabolic processGO:0042437
GO:0042437
indoleacetic acid catabolic process
GO:0042437 provides the biological-process context for bacterial oxidative indole-3-acetic acid degradation.
PMID:32999461
A single bacterial genus maintains root growth in a complex microbiome.
Demonstrates that a conserved auxin-degradation (iad) operon in Variovorax strains is necessary and sufficient for reverting auxin- and microbiome-induced root growth inhibition.
We identify an auxin-degradation operon that is conserved in all available genomes of Variovorax and is necessary and sufficient for the reversion of root growth inhibition.
PMID:36266335
Diverse MarR bacterial regulators of auxin catabolism in the plant microbiome.
Demonstrates that co-expression of iadC with iadD and iadE is required to revert Arthrobacter-dependent root growth inhibition in the rhizosphere, characterizes the IAA-responsive MarR-family repressor IadR binding upstream of iadA, identifies iotA/iadA and iorB/iadB as exclusive markers of iad-like operons, and shows by 13C6-IAA metabolomics that the iad pathway degrades IAA via dioxindole-3-acetic acid, isatin, and isatinic acid to anthranilic acid.
The intermediates dioxindole, isatin and isatinic acid, and the product anthranilic acid were all detected and thus produced in the bacterial cultures. Importantly, catechol, the main product of the iac IAA degradation, was not detected in any of the V. paradoxus CL14 samples.
PMID:37459330
Structural and biochemical characterization of the key components of an auxin degradation operon from the rhizosphere bacterium Variovorax.
Resolves the crystal structures and biochemical activities of the Variovorax paradoxus IadK2 periplasmic IAA-binding protein (and its non-IAA-binding paralog IadK3), the IadD/IadE Rieske dioxygenase complex, and the IadC ferredoxin-NAD+ reductase.
Together, these data suggest that IAA was converted to oxIAA by the dioxygenase system composed of the IadD/E dioxygenase and the IadC reductase (Fig 5E).
PMID:21183664
Complete genome sequence of the metabolically versatile plant growth-promoting endophyte Variovorax paradoxus S110.
Establishes the complete genome sequence of Variovorax paradoxus S110 hosting the iad gene cluster (Vapar_1489 to Vapar_1494).
The complete genome sequence of V. paradoxus S110 is composed of 6,754,997 bp with 6,279 predicted protein-coding sequences within two circular chromosomes.
file:VARPS/iadD/iadD-ai-review.yaml
Variovorax paradoxus S110 iadD gene review
C5CSP6 (Vapar_1493) encodes the catalytic alpha subunit IadD of the indole-3-acetic acid Rieske dioxygenase.
file:VARPS/iadE/iadE-ai-review.yaml
Variovorax paradoxus S110 iadE gene review
C5CSP7 (Vapar_1494) encodes the structural beta subunit IadE of the heterohexameric IadD/IadE dioxygenase complex.
file:VARPS/iadC/iadC-ai-review.yaml
Variovorax paradoxus S110 iadC gene review
C5CSP5 (Vapar_1492) encodes the Class IA FMN/[2Fe-2S] ferredoxin-NAD+ reductase component IadC that supplies electrons to IadD/IadE.
file:VARPS/iadR/iadR-ai-review.yaml
Variovorax paradoxus S110 iadR gene review
C5CSP2 (Vapar_1489) encodes the IAA-sensing MarR-family transcriptional repressor IadR.
file:VARPD/iadK2/iadK2-ai-review.yaml
Variovorax paradoxus iadK2 gene review
A0A0H2MF78 (VPARA_32110) encodes the high-affinity periplasmic subcluster B-III ABC transporter IAA-binding protein IadK2.
file:VARPD/iadK3/iadK3-ai-review.yaml
Variovorax paradoxus iadK3 gene review
A0A0H2LZ84 (VPARA_32100) encodes the paralogous subcluster B-III periplasmic solute-binding protein IadK3 that lacks IAA binding due to pocket substitutions (S104V/W172L equivalent) and weakly associates with oxIAA.
file:VARPD/iadA/iadA-ai-review.yaml
Variovorax paradoxus iadA gene review
A0A0H2MF87 (VPARA_32210) encodes the TPP- and [4Fe-4S]-binding alpha subunit IadA (IotA) of the iad-operon 2-oxoacid:ferredoxin oxidoreductase complex.
file:VARPD/iadB/iadB-ai-review.yaml
Variovorax paradoxus iadB gene review
A0A0H2LZ92 (VPARA_32200) encodes the beta subunit IadB (IorB) of the iad-operon 2-oxoacid:ferredoxin oxidoreductase complex.
file:VARPD/iadI/iadI-ai-review.yaml
Variovorax paradoxus iadI gene review
A0A0H2M433 (VPARA_32130, kynB2) encodes the putative cyclic-amide amidohydrolase / isatin hydrolase IadI involved in downstream hydrolytic processing of oxidized IAA intermediates (such as isatin to isatinic acid) en route to anthranilic acid.
7Nodes
6Parts
0Variant Sets
0Variants
6Annotons
5Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:bacterial_iad_auxin_catabolism 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

7 gene-function check(s) reflected in core functions · 0 conflict(s) · 7 evidence or coverage gap(s) (16 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
iadR_repressor_activity iadR (Variovorax paradoxus S110)
UniProtKB:C5CSP2
Family Representative 		DNA-binding transcription repressor activity
GO:0001217 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
iadK2_auxin_binding_activity iadK2 (Variovorax paradoxus)
UniProtKB:A0A0H2MF78
Family Representative 		auxin binding
GO:0010011 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
iadC_ferredoxin_activity iadC (Variovorax paradoxus S110)
UniProtKB:C5CSP5
Family Representative 		ferredoxin-NAD+ reductase activity
GO:0008860 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
iadDE_dioxygenase_activity PROTEIN_COMPLEX
Gene 		oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of two atoms of oxygen into one donor
GO:0016708 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
iadDE_dioxygenase_activity/iadD_alpha_unit iadD (Variovorax paradoxus S110)
UniProtKB:C5CSP6
Family Representative 		oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of two atoms of oxygen into one donor
GO:0016708 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
iadAB_oxidoreductase_activity PROTEIN_COMPLEX
Gene 		oxidoreductase activity, acting on the aldehyde or oxo group of donors
GO:0016903 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
iadAB_oxidoreductase_activity/iadA_alpha_unit iadA (Variovorax paradoxus)
UniProtKB:A0A0H2MF87
Family Representative 		oxidoreductase activity, acting on the aldehyde or oxo group of donors
GO:0016903 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
iadAB_oxidoreductase_activity/iadB_beta_unit iadB (Variovorax paradoxus)
UniProtKB:A0A0H2LZ92
Family Representative 		oxidoreductase activity, acting on the aldehyde or oxo group of donors
GO:0016903 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
iadI_cyclic_amidohydrolase_activity iadI (Variovorax paradoxus)
UniProtKB:A0A0H2M433
Family Representative 		hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides
GO:0016812 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
iadR_repressor_activity IadR MarR-family IAA-sensing repressors
Family 		DNA-binding transcription repressor activity
GO:0001217 		Family Id Missing
The family has no identifier linking it to a curated family review.
iadK2_auxin_binding_activity IadK2 subcluster B-III periplasmic IAA-binding proteins
Family 		auxin binding
GO:0010011 		Family Id Missing
The family has no identifier linking it to a curated family review.
iadC_ferredoxin_activity IadC Class IA FMN/[2Fe-2S] dioxygenase reductases
Family 		ferredoxin-NAD+ reductase activity
GO:0008860 		Family Id Missing
The family has no identifier linking it to a curated family review.
iadD_alpha_unit IadD aromatic-ring-hydroxylating dioxygenase alpha subunits
Family 		oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of two atoms of oxygen into one donor
GO:0016708 		Family Id Missing
The family has no identifier linking it to a curated family review.
iadA_alpha_unit IadA (IotA) 2-oxoacid:ferredoxin oxidoreductase alpha subunits
Family 		oxidoreductase activity, acting on the aldehyde or oxo group of donors
GO:0016903 		Family Id Missing
The family has no identifier linking it to a curated family review.
iadB_beta_unit IadB (IorB) 2-oxoacid:ferredoxin oxidoreductase beta subunits
Family 		oxidoreductase activity, acting on the aldehyde or oxo group of donors
GO:0016903 		Family Id Missing
The family has no identifier linking it to a curated family review.
iadI_cyclic_amidohydrolase_activity IadI (KynB2) iad-operon cyclic-amide amidohydrolases
Family 		hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides
GO:0016812 		Family Id Missing
The family has no identifier linking it to a curated family review.

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.

  • iadR_regulation_step ⊣ iadDE_dioxygenase_step [input]
    iadR_regulation_step is a negative regulator with no upstream edge (not described as feedback)

Gene-review completeness (8/8 grounded genes reviewed)

8 complete review(s) · 0 with deep research · 0 missing review · 8 reviewed but lacking deep research

Gene Review Complete Deep research
iadA A0A0H2MF87 ✓ ✓ ✗
iadB A0A0H2LZ92 ✓ ✓ ✗
iadC C5CSP5 ✓ ✓ ✗
iadD C5CSP6 ✓ ✓ ✗
iadE C5CSP7 ✓ ✓ ✗
iadI A0A0H2M433 ✓ ✓ ✗
iadK2 A0A0H2MF78 ✓ ✓ ✗
iadR C5CSP2 ✓ ✓ ✗

Details

Bacterial iad-type aerobic indole-3-acetic acid catabolismMetabolic Pathwaybacterial_iad_auxin_catabolism
indoleacetic acid catabolic processGO:0042437

Grounded on the Variovorax paradoxus strain S110 (NCBITaxon:543728) exemplars C5CSP2 (IadR, Vapar_1489), C5CSP5 (IadC, Vapar_1492), C5CSP6 (IadD, Vapar_1493), and C5CSP7 (IadE, Vapar_1494) together with the syntenic Variovorax paradoxus strain TBEA6 (NCBITaxon:34073, Proteomes:UP000035170) iad operon proteins A0A0H2MF78 (IadK2, VPARA_32110), A0A0H2LZ84 (IadK3, VPARA_32100), A0A0H2MF87 (IadA, VPARA_32210), A0A0H2LZ92 (IadB, VPARA_32200), and A0A0H2M433 (IadI/KynB2, VPARA_32130), with experimental biochemical, structural, genetic, and metabolomic characterization performed in the orthologous V. paradoxus strain CL14 (PMID:32999461, PMID:36266335, PMID:37459330). The co-encoded paralogous B-III solute-binding protein IadK3 (A0A0H2LZ84) lacks IAA-binding activity due to pocket substitutions (Val100 and Leu168, corresponding to S104V and W172L of IadK2) and weakly associates with 2-oxindole-3-acetic acid (oxIAA). The inner-membrane ABC transporter permease/ATPase subunits (IadG, IadH, IadJ) and CoA-transferase/acyl-CoA subunit (IadF) are not yet curated as separate module nodes.

Connections

IadR binds the DNA operator site between iadR and iadA to repress transcription of the iad operon in the absence of IAA; binding of indole-3-acetic acid to IadR relieves repression across the operon.
Periplasmic IadK2 captures extracellular indole-3-acetic acid with nanomolar affinity for ABC transporter-mediated import to supply intracellular IAA to the IadD/IadE dioxygenase complex.
IadC transfers electrons via its [2Fe-2S] cluster to the Rieske cluster of IadD to support dioxygen activation and IAA oxidation.
Initial oxygenation of IAA by IadD/IadE produces 2-hydroxyindole-3-acetic acid / 2-oxindole-3-acetic acid, which is further oxidized via dioxindole-3-acetic acid and processed by downstream iad enzymes including IadA/IadB toward isatin and isatinic acid.
Downstream oxidative processing of IAA intermediates generates cyclic-amide indole derivatives such as isatin, which is proposed to be hydrolyzed by IadI to isatinic acid en route to anthranilic acid.
Part 1: auxin-responsive transcriptional derepression of the iad operon
IadR IAA-responsive transcriptional repressionRegulatory StepiadR_regulation_step

Annotons

IadR MarR-family DNA-binding transcription repressor
iadR_repressor_activity
Participant: Family: IadR MarR-family IAA-sensing repressors
Family:
IadR MarR-family IAA-sensing repressors
Representative Members: iadR (Variovorax paradoxus S110)UniProtKB:C5CSP2

Function

DNA-binding transcription repressor activityGO:0001217

Represses transcription of the iad operon in the absence of auxin and dissociates from operator DNA upon binding indole-3-acetic acid.

Part 2: high-affinity periplasmic capture of indole-3-acetic acid for ABC transporter import
IadK2 periplasmic indole-3-acetic acid captureTransport StepiadK2_periplasmic_uptake_step

Annotons

IadK2 subcluster B-III periplasmic IAA-binding protein
iadK2_auxin_binding_activity
Participant: Family: IadK2 subcluster B-III periplasmic IAA-binding proteins
Family:
IadK2 subcluster B-III periplasmic IAA-binding proteins
Representative Members: iadK2 (Variovorax paradoxus)UniProtKB:A0A0H2MF78

Function

auxin bindingGO:0010011

Selectively binds extracellular indole-3-acetic acid in the periplasm with nanomolar affinity to facilitate ABC transporter-mediated auxin import into the bacterial cell.

Part 3: NADH-dependent ferredoxin electron transfer to the IadD/IadE oxygenase complex
IadC ferredoxin-NAD+ reductase electron transferReactioniadC_electron_transfer_step

Annotons

IadC ferredoxin-NAD+ reductase
iadC_ferredoxin_activity
Participant: Family: IadC Class IA FMN/[2Fe-2S] dioxygenase reductases
Family:
IadC Class IA FMN/[2Fe-2S] dioxygenase reductases
Representative Members: iadC (Variovorax paradoxus S110)UniProtKB:C5CSP5

Function

ferredoxin-NAD+ reductase activityGO:0008860
Substrates: NADH
Products: NAD+

Oxidizes NADH and shuttles electrons via FMN and its C-terminal [2Fe-2S] ferredoxin domain to the Rieske [2Fe-2S] cluster of IadD.

Part 4: oxidative indole-3-acetic acid hydroxylation and ring conversion
IadD/IadE indole-3-acetic acid Rieske dioxygenaseReactioniadDE_dioxygenase_step

Annotons

IadD/IadE heterohexameric indole-3-acetic acid Rieske dioxygenase
iadDE_dioxygenase_activity
Participant: Protein Complex: IadD/IadE indole-3-acetic acid Rieske dioxygenase heterohexamer
Protein Complex:
IadD/IadE indole-3-acetic acid Rieske dioxygenase heterohexamerGO:1902494
Active units:
IadD catalytic alpha subunitalpha3
Participant: Family: IadD aromatic-ring-hydroxylating dioxygenase alpha subunits
Family:
IadD aromatic-ring-hydroxylating dioxygenase alpha subunits
Representative Members: iadD (Variovorax paradoxus S110)UniProtKB:C5CSP6
Role: Catalytic alpha subunit housing the Rieske [2Fe-2S] cluster, mononuclear non-heme iron center, and IAA substrate-binding pocket.
Function:
oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of two atoms of oxygen into one donorGO:0016708
IadE structural beta subunitbeta3
Participant: Family: IadE aromatic-ring-hydroxylating dioxygenase beta subunits
Family:
IadE aromatic-ring-hydroxylating dioxygenase beta subunits
Representative Members: iadE (Variovorax paradoxus S110)UniProtKB:C5CSP7
Role: Structural beta subunit forming the trimeric stem base of the alpha3-beta3 heterohexamer; contributes to holoenzyme assembly without autonomous catalytic activity.

Function

oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of two atoms of oxygen into one donorGO:0016708
Substrates: indole-3-acetic acid dioxygen
Products: 2-oxindole-3-acetic acid

Catalyzes the committed oxidative conversion of indole-3-acetic acid to 2-oxindole-3-acetic acid at the mononuclear non-heme iron active site of the alpha3-beta3 IadD/IadE holoenzyme.

Part 5: TPP- and [4Fe-4S]-dependent oxidative side-chain cleavage of oxidized indole intermediates
IadA/IadB 2-oxoacid:ferredoxin oxidoreductase side-chain processingReactioniadAB_oxidoreductase_step

Annotons

IadA/IadB heterodimeric 2-oxoacid:ferredoxin oxidoreductase
iadAB_oxidoreductase_activity
Participant: Protein Complex: IadA/IadB indolepyruvate/2-oxoacid ferredoxin oxidoreductase complex
Protein Complex:
IadA/IadB indolepyruvate/2-oxoacid ferredoxin oxidoreductase complexGO:1902494
Active units:
IadA catalytic TPP/[4Fe-4S] alpha subunitalpha
Participant: Family: IadA (IotA) 2-oxoacid:ferredoxin oxidoreductase alpha subunits
Family:
IadA (IotA) 2-oxoacid:ferredoxin oxidoreductase alpha subunits
Representative Members: iadA (Variovorax paradoxus)UniProtKB:A0A0H2MF87
Role: Alpha subunit housing the thiamine pyrophosphate (TPP) binding fold and C-terminal [4Fe-4S] ferredoxin domain.
Function:
oxidoreductase activity, acting on the aldehyde or oxo group of donorsGO:0016903
IadB catalytic beta subunitbeta
Participant: Family: IadB (IorB) 2-oxoacid:ferredoxin oxidoreductase beta subunits
Family:
IadB (IorB) 2-oxoacid:ferredoxin oxidoreductase beta subunits
Representative Members: iadB (Variovorax paradoxus)UniProtKB:A0A0H2LZ92
Role: Beta subunit containing the PF01558 oxidoreductase catalytic domain and C-terminal DUF6537 domain.
Function:
oxidoreductase activity, acting on the aldehyde or oxo group of donorsGO:0016903

Function

oxidoreductase activity, acting on the aldehyde or oxo group of donorsGO:0016903

Heterodimeric TPP/[4Fe-4S] oxidoreductase complex (IadA/IadB) that serves as an exclusive hallmark of iad-like operons and participates in downstream oxidative processing of IAA intermediates toward anthranilic acid, although its specific in vivo 2-oxoacid substrate and product have not yet been biochemically established.

Part 6: putative hydrolytic ring opening of cyclic-amide oxidized indole intermediates (such as isatin to isatinic acid) en route to anthranilic acid
IadI putative cyclic-amide / isatin hydrolase stepReactioniadI_cyclic_amidohydrolase_step

Annotons

IadI putative cyclic-amide amidohydrolase / isatin hydrolase
iadI_cyclic_amidohydrolase_activity
Participant: Family: IadI (KynB2) iad-operon cyclic-amide amidohydrolases
Family:
IadI (KynB2) iad-operon cyclic-amide amidohydrolases
Representative Members: iadI (Variovorax paradoxus)UniProtKB:A0A0H2M433

Function

hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidesGO:0016812
Substrates: isatin
Products: isatinic acid

Putative metal-dependent cyclic-amide amidohydrolase (PF04199 / IPR007325) proposed to hydrolyze the heterocyclic lactam ring of isatin to isatinic acid en route to anthranilic acid in the iad pathway.