RBOHD

UniProt ID: Q9FIJ0
Organism: Arabidopsis thaliana
Review Status: DRAFT
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Gene Description

RBOHD (Respiratory burst oxidase homolog protein D; AtrbohD) is a plasma-membrane, calcium-dependent NADPH oxidase of the RBOH/NOX (gp91phox homolog) family. The 921-residue, six-transmembrane protein carries an N-terminal cytoplasmic regulatory region with two EF-hand calcium-binding motifs and a C-terminal cytoplasmic FAD- and NADPH-binding ferredoxin reductase-like module. It transfers electrons from cytosolic NADPH across the plasma membrane to molecular oxygen, producing apoplastic superoxide that rapidly dismutates to hydrogen peroxide. RBOHD is the principal source of the extracellular oxidative ("respiratory") burst in plant immunity. Upon perception of pathogen-associated molecular patterns by surface receptors such as FLS2, it is activated by a rise in cytosolic calcium (via its EF-hands) and by phosphorylation by receptor-like cytoplasmic kinases (notably BIK1) and other kinases (SIK1, calcium-dependent protein kinases), while being held in check by negative regulators such as the kinase PBL13. The reactive oxygen species it produces act in PAMP-triggered immunity, in the regulation and spatial restriction of hypersensitive cell death, in long-distance ROS-wave systemic signaling, and in abscisic acid- and calcium-dependent stomatal closure. RBOHD also contributes ROS to abiotic stress responses including wounding, heat, UV-B, osmotic/cell-wall-integrity signaling, and low-oxygen stress. It is most abundant in roots and is expressed in mesophyll and guard cells.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0004601 peroxidase activity
IEA
GO_REF:0000002
REMOVE
Summary: RBOHD is a superoxide-generating NADPH oxidase, not a peroxidase. This IEA derives from the gp91phox/cytochrome-b245 (Cyt_b245) InterPro signature (IPR013623) and the associated UniProt "Peroxidase" keyword, which is misleading for RBOH proteins. The enzyme reduces O2 to superoxide using electrons from NADPH; it does not reduce hydrogen peroxide.
Reason: The catalytic activity of RBOHD is electron transfer from NADPH to O2 to generate superoxide (and downstream H2O2 by dismutation), not peroxidase activity. The InterPro-derived peroxidase keyword is a known mis-mapping for the gp91phox family and over-annotates the gene. The informative catalytic term is GO:0016175 (added as NEW).
Supporting Evidence:
PMID:11756663
our demonstration that an NADPH oxidase subunit is required for ROI production confirms Doke's original suggestion that O is the first ROI produced
GO:0005509 calcium ion binding
IEA
GO_REF:0000002
ACCEPT
Summary: RBOHD contains two canonical N-terminal EF-hand calcium-binding domains (UniProt residues 253-288 and 297-332, with Ca2+ coordinated by residues 266/268/270/272/277) and is a calcium-dependent NADPH oxidase. Calcium binding to these EF-hands is integral to its activation.
Reason: Well supported by conserved EF-hand domains/Ca2+ binding sites in UniProt and by the calcium-dependence of RBOH oxidase activity. This is a core molecular function contributing to activity regulation.
Supporting Evidence:
PMID:24629339
Here we show that the receptor-like cytoplasmic kinase BIK1, a component of the FLS2 immune receptor complex, not only positively regulates flg22-triggered calcium influx but also directly phosphorylates the NADPH oxidase RbohD at specific sites in a calcium-independent manner to enhance ROS generation.
file:ARATH/RBOHD/RBOHD-deep-research-falcon.md
RBOHD is activated by direct Ca2+ binding to EF-hands and by phosphorylation
GO:0006952 defense response
IEA
GO_REF:0000117
ACCEPT
Summary: RBOHD generates the apoplastic ROS burst central to plant immune responses; rbohD mutants fail to accumulate ROS during pathogen defense. This electronic annotation is consistent with strong experimental evidence (see also the IMP defense response annotation below).
Reason: Defense response is a well-established core biological process for RBOHD, supported by mutant phenotypes during pathogen interactions.
Supporting Evidence:
PMID:11756663
AtrbohD and AtrbohF are required for accumulation of reactive oxygen intermediates in the plant defense response
file:ARATH/RBOHD/RBOHD-deep-research-falcon.md
major NADPH oxidase responsible for pathogen-triggered ROS
GO:0016020 membrane
IEA
GO_REF:0000120
ACCEPT
Summary: RBOHD is a multi-pass (six transmembrane helix) integral membrane protein, specifically of the plasma membrane. This generic membrane term is correct but less informative than the plasma membrane annotation.
Reason: True location but generic; the more specific plasma membrane annotation (GO:0005886) captures the functional compartment. Retained as accurate but non-core relative to plasma membrane.
Supporting Evidence:
PMID:24629339
directly phosphorylates the NADPH oxidase RbohD
GO:0016491 oxidoreductase activity
IEA
GO_REF:0000002
ACCEPT
Summary: RBOHD is an oxidoreductase that transfers electrons from NADPH to O2. This is a very general parent of the specific superoxide-generating NADPH oxidase activity.
Reason: Correct but high-level; acceptable as a broad IEA parent of the informative term GO:0016175. Not the core descriptor on its own.
Supporting Evidence:
PMID:11756663
AtrbohD and AtrbohF, encoding probable components of a plant NADPH oxidase
file:ARATH/RBOHD/RBOHD-deep-research-falcon.md
catalyzes **electron transfer from cytosolic NADPH to molecular oxygen (O2)** to generate **superoxide (O2•−)** in the **apoplast**, which can subsequently form **H2O2**
GO:0050664 oxidoreductase activity, acting on NAD(P)H, oxygen as acceptor
IEA
GO_REF:0000002
ACCEPT
Summary: This term correctly describes RBOHD as an NAD(P)H-dependent oxidoreductase using oxygen as electron acceptor, which is precisely the RBOH oxidase chemistry. It is the immediate parent of the superoxide-generating term GO:0016175.
Reason: Accurate and reasonably specific; consistent with the NADPH-binding ferredoxin-reductase module and O2-reducing oxidase activity. The product-specific child term GO:0016175 is added as NEW.
Supporting Evidence:
PMID:11756663
an NADPH oxidase subunit is required for ROI production
file:ARATH/RBOHD/RBOHD-deep-research-falcon.md
a catalytic C-terminal core with FAD- and NADPH-binding domains
GO:0098869 cellular oxidant detoxification
IEA
GO_REF:0000108
REMOVE
Summary: This term is inferred logically from the spurious peroxidase MF (GO:0004601 to GO:0098869). RBOHD generates reactive oxygen species for signaling; it does not detoxify cellular oxidants. The annotation is essentially backwards with respect to the protein's biology.
Reason: RBOHD is a ROS-producing enzyme, not an antioxidant/detoxifying enzyme. The inference depends on the incorrect peroxidase activity assignment, which is itself being removed.
Supporting Evidence:
PMID:19726575
Functional RBOHD causes marked extracellular hydrogen peroxide accumulation
GO:0005794 Golgi apparatus
HDA
PMID:22430844
Isolation and proteomic characterization of the Arabidopsis ...
MARK AS OVER ANNOTATED
Summary: A Golgi assignment from high-throughput organellar proteomics. For a multi-pass plasma-membrane oxidase, a Golgi signal most plausibly reflects transit through the secretory pathway or co-fractionation rather than a functional Golgi pool. The functional location is the plasma membrane.
Reason: High-throughput proteomic localization without functional support; inconsistent with the established plasma-membrane site of RBOHD action. Likely reflects biosynthetic trafficking or proteomic co-fractionation.
Supporting Evidence:
PMID:22430844
Isolation and proteomic characterization of the Arabidopsis Golgi
GO:0005886 plasma membrane
HDA
PMID:22923678
Putative glycosyltransferases and other plant Golgi apparatu...
ACCEPT
Summary: The plasma membrane is the functional location of RBOHD. It is a multi-pass plasma-membrane NADPH oxidase that releases superoxide into the apoplast, where it acts together with plasma-membrane receptor complexes (FLS2/BIK1) in immune signaling.
Reason: Strongly supported by proteomics and by the abundant literature placing RBOHD in plasma-membrane PRR complexes; this is the core cellular location for its function.
Supporting Evidence:
PMID:24629339
BIK1, a component of the FLS2 immune receptor complex
PMID:22923678
plant Golgi apparatus proteins are revealed by LOPIT proteomics
file:ARATH/RBOHD/RBOHD-deep-research-falcon.md
RBOHD is a plasma membrane-localized NADPH oxidase that produces ROS into the apoplast
GO:0071456 cellular response to hypoxia
HEP
PMID:31519798
Integrative Analysis from the Epigenome to Translatome Uncov...
KEEP AS NON CORE
Summary: RBOHD expression/regulation is captured in an integrative epigenome-to-translatome study of transient stress that includes hypoxia. Consistent with a role for RBOH-derived ROS in low-oxygen responses (cf. HRU1/ROP2/RbohD module under anoxia), this peripheral, expression-pattern based annotation is plausible but not a core function.
Reason: Expression-pattern (HEP) evidence from a high-throughput stress study; supports involvement in hypoxia responses but as a peripheral process rather than a defining function. Concordant with independent anoxia evidence (PMID:27251529).
Supporting Evidence:
PMID:27251529
HRU1 interacts with proteins that induce ROS production, the GTPase ROP2 and the NADPH oxidase RbohD, pointing to the existence of a low-oxygen-specific mechanism for the modulation of ROS levels
GO:0009536 plastid
HDA
PMID:28887381
Global Analysis of Membrane-associated Protein Oligomerizati...
REMOVE
Summary: A plastid assignment from a global membrane-protein correlation-profiling study. RBOHD is a plasma-membrane oxidase; a plastid location is not supported by any functional study and most likely reflects co-fractionation/contamination in the high-throughput dataset.
Reason: No functional or targeted experimental support for a plastid pool of RBOHD; inconsistent with its plasma-membrane topology and apoplastic ROS output. Likely a proteomic artifact.
Supporting Evidence:
PMID:28887381
Global Analysis of Membrane-associated Protein Oligomerization Using Protein Correlation Profiling
GO:0005634 nucleus
ISM
GO_REF:0000122
REMOVE
Summary: A purely computational subcellular-localization prediction (AtSubP). A six-transmembrane plasma-membrane oxidase is not expected to localize to the nucleus, and no experimental evidence supports a nuclear RBOHD.
Reason: Sequence-based prediction (ISM) contradicted by the membrane topology and experimentally established plasma-membrane localization. No supporting functional evidence.
Supporting Evidence:
PMID:22923678
plant Golgi apparatus proteins are revealed by LOPIT proteomics
GO:0005515 protein binding
IPI
PMID:28696275
A Lectin Receptor-Like Kinase Mediates Pattern-Triggered Sal...
MARK AS OVER ANNOTATED
Summary: Refers to functional interaction within pattern-triggered immunity signaling; the lectin receptor-like kinase LecRK-IX.2 induces RBOHD phosphorylation (likely via calcium-dependent protein kinases) to trigger ROS. "Protein binding" is uninformative about RBOHD's actual molecular function.
Reason: Generic protein binding conveys no specific functional information. The biologically meaningful content (regulation of RBOHD ROS output by upstream immune kinases) is captured in the core_functions and process annotations rather than by GO:0005515.
Supporting Evidence:
PMID:28696275
LecRK-IX.2 is capable of inducing RbohD phosphorylation, likely by recruiting calcium-dependent protein kinases to trigger ROS production in Arabidopsis
GO:0005515 protein binding
IPI
PMID:24629339
The FLS2-associated kinase BIK1 directly phosphorylates the ...
MARK AS OVER ANNOTATED
Summary: This IPI records the interaction of RBOHD with BIK1 and FLS2. BIK1 directly phosphorylates RBOHD to enhance ROS during immunity. While biologically important, the bare "protein binding" term is uninformative.
Reason: The interaction with BIK1/FLS2 is a key activation mechanism, but GO:0005515 does not capture it usefully. The functional relationship (kinase-mediated activation of RBOHD) is documented in notes and core_functions; a specific kinase-binding term would be preferable but is not added here to avoid over-fitting.
Supporting Evidence:
PMID:24629339
the receptor-like cytoplasmic kinase BIK1, a component of the FLS2 immune receptor complex ... directly phosphorylates the NADPH oxidase RbohD at specific sites
file:ARATH/RBOHD/RBOHD-deep-research-falcon.md
In PTI, PRRs such as FLS2/EFR activate downstream cytoplasmic kinases (e.g., BIK1) that phosphorylate RBOHD to drive a rapid ROS burst
GO:0005515 protein binding
IPI
PMID:26432875
PBL13 Is a Serine/Threonine Protein Kinase That Negatively R...
MARK AS OVER ANNOTATED
Summary: Records the interaction of RBOHD with the negative-regulatory kinase PBL13 (split-luciferase complementation), which is disrupted by flagellin treatment. Informative biologically but not captured by the generic term.
Reason: Generic protein binding is uninformative. The PBL13 interaction is a negative-regulatory mechanism for RBOHD ROS production, documented in notes; GO:0005515 itself should not be treated as a core molecular function.
Supporting Evidence:
PMID:26432875
PBL13 is able to associate with the nicotinamide adenine dinucleotide phosphate, reduced oxidase RESPIRATORY BURST OXIDASE HOMOLOG PROTEIN D (RBOHD) by split-luciferase complementation assay, and this association is disrupted by flagellin treatment
GO:0005515 protein binding
IPI
PMID:27251529
Universal stress protein HRU1 mediates ROS homeostasis under...
MARK AS OVER ANNOTATED
Summary: Records interaction of RBOHD with the universal stress protein HRU1 (and ROP2) in modulating ROS production under anoxia. Biologically meaningful but uninformative as a bare protein-binding term.
Reason: Generic protein binding lacks specificity. The HRU1/ROP2 interaction links oxygen sensing to RBOHD ROS output under low oxygen; documented in notes rather than via GO:0005515.
Supporting Evidence:
PMID:27251529
HRU1 interacts with proteins that induce ROS production, the GTPase ROP2 and the NADPH oxidase RbohD
GO:0072593 reactive oxygen species metabolic process
IGI
PMID:26704641
Arabidopsis HY1-Modulated Stomatal Movement: An Integrative ...
ACCEPT
Summary: RBOHD-derived ROS are required for ABA/HY1-ABI4-dependent stomatal closure; genetic interaction places RBOHD upstream of the ROS levels that mediate stomatal movement. Consistent with RBOHD as a primary ROS generator.
Reason: Well supported; RBOHD is a major contributor to cellular ROS metabolism, here in the context of ABA-dependent stomatal regulation.
Supporting Evidence:
PMID:26704641
the promotion of ABA-triggered up-regulation of RbohD abundance and reactive oxygen species (ROS) levels in the hy1 mutant was almost fully blocked by the mutation of ABI4
GO:0007231 osmosensory signaling pathway
IMP
PMID:22422940
Osmosensitive changes of carbohydrate metabolism in response...
KEEP AS NON CORE
Summary: In cellulose-biosynthesis-inhibition experiments, rbohDF mutants fail to show the osmosensitive metabolic changes, implicating RBOHD/F-derived ROS in osmo/cell-wall-integrity signaling.
Reason: Supported by mutant phenotype, but this is a specialized, peripheral signaling context relative to RBOHD's central immune/ROS-burst role. Retained as a genuine but non-core process.
Supporting Evidence:
PMID:22422940
osmotic support does not suppress CBI-induced metabolic changes in seedlings impaired in ... reactive oxygen species production (respiratory burst oxidase homolog DF [rbohDF])
GO:0033500 carbohydrate homeostasis
IMP
PMID:22422940
Osmosensitive changes of carbohydrate metabolism in response...
KEEP AS NON CORE
Summary: The same study links RBOHD/F-derived ROS to osmosensitive control of carbohydrate metabolism after cellulose biosynthesis inhibition. The effect on carbohydrate homeostasis is indirect and downstream of the osmo-signaling role.
Reason: Indirect, context-specific phenotype; ROS from RBOHD feed into an osmosensitive regulatory circuit that affects carbohydrate metabolism, but this is peripheral to the protein's core ROS-generating immune function.
Supporting Evidence:
PMID:22422940
carbohydrate metabolism is responsive to changes in cellulose biosynthesis activity and turgor pressure
GO:0009611 response to wounding
IEP
PMID:21419340
Calmodulin-dependent activation of MAP kinase for ROS homeos...
KEEP AS NON CORE
Summary: The Ca2+/CaM-MPK8-MKK3 wound-signaling pathway negatively regulates ROS accumulation through control of RbohD expression, linking RBOHD to wound-induced ROS homeostasis.
Reason: RBOHD participates in wound-induced ROS homeostasis (as a regulated ROS source), but the evidence is expression-pattern based (IEP) and the process is peripheral to its central immune ROS-burst function.
Supporting Evidence:
PMID:21419340
The MPK8 pathway negatively regulates ROS accumulation through controlling expression of the Rboh D gene
GO:0072593 reactive oxygen species metabolic process
IMP
PMID:11756663
Arabidopsis gp91phox homologues AtrbohD and AtrbohF are requ...
ACCEPT
Summary: rbohD insertion mutants eliminate the majority of pathogen-induced ROS, demonstrating that RBOHD is the principal generator of the defense oxidative burst. This is a core process annotation.
Reason: Strong genetic evidence that RBOHD drives ROS metabolic process (the extracellular oxidative burst) during defense; a defining function.
Supporting Evidence:
PMID:11756663
The AtrbohD gene is required for most of the ROI observed after inoculation with avirulent Pst
GO:0072593 reactive oxygen species metabolic process
TAS
PMID:15705948
Different signaling and cell death roles of heterotrimeric G...
ACCEPT
Summary: RBOHD is part of the Arabidopsis ROS gene network and contributes ROS in the oxidative stress response (including ozone/G-protein-mediated responses). Consistent with its established role in ROS production.
Reason: TAS annotation consistent with the well-documented role of RBOHD as a generator of signaling ROS; duplicate aspect of the core ROS metabolic process annotation.
Supporting Evidence:
PMID:11756663
extracellular ROI production in Arabidopsis requires Atrboh function
GO:0043069 negative regulation of programmed cell death
IGI
PMID:16170317
Pathogen-induced, NADPH oxidase-derived reactive oxygen inte...
ACCEPT
Summary: RBOHD-derived ROS suppress the spread of hypersensitive cell death into cells surrounding infection sites, antagonizing salicylic acid-dependent pro-death signals. Thus RBOHD limits cell-death spread even though its ROS can also trigger localized death.
Reason: Supported by genetic evidence; an established (if context-dependent) role of RBOHD in restricting programmed cell death spread during the immune response.
Supporting Evidence:
PMID:16170317
the subsequent oxidative burst can suppress cell death in cells surrounding sites of NADPH oxidase activation
PMID:19726575
functional RBOHD triggers death in cells that are damaged by fungal infection but simultaneously inhibits death in neighboring cells
GO:0016174 NAD(P)H oxidase H2O2-forming activity
IMP
PMID:19726575
Dual roles of reactive oxygen species and NADPH oxidase RBOH...
MODIFY
Summary: RBOHD is a NADPH oxidase whose immediate enzymatic product is superoxide; the measured apoplastic H2O2 arises by (spontaneous or SOD-catalyzed) dismutation of that superoxide. The more accurate catalytic term is GO:0016175 "superoxide-generating NAD(P)H oxidase activity". The H2O2-forming term reflects the downstream detected species rather than the primary reaction.
Reason: The proximal product is superoxide (PMID:11756663), so the product-specific MF should be the superoxide-generating activity. H2O2 is formed secondarily by dismutation, making GO:0016174 a less accurate descriptor of the catalyzed reaction.
Supporting Evidence:
PMID:11756663
O is the first ROI produced
PMID:19726575
Functional RBOHD causes marked extracellular hydrogen peroxide accumulation
GO:0050832 defense response to fungus
IMP
PMID:19726575
Dual roles of reactive oxygen species and NADPH oxidase RBOH...
ACCEPT
Summary: rbohD knockout alters ROS accumulation and cell-death patterns upon infection with the necrotrophic fungus Alternaria brassicicola, demonstrating involvement in antifungal defense (with dual, position- dependent effects on cell death).
Reason: Supported by mutant phenotype in a defined fungal pathosystem; a genuine, if context-dependent, defense-against-fungus role for RBOHD.
Supporting Evidence:
PMID:19726575
a rbohD knockout mutant exhibits increased spread of cell death at the macroscopic level upon inoculation with the fungus Alternaria brassicicola
GO:0009408 response to heat
IMP
PMID:15923322
Heat stress phenotypes of Arabidopsis mutants implicate mult...
KEEP AS NON CORE
Summary: atrbohD mutants show (weaker) defects in acquired thermotolerance, implicating RBOHD-derived ROS/oxidative-burst signaling in the heat-stress response among multiple contributing pathways.
Reason: Supported by mutant phenotype but the effect is relatively weak and this abiotic-stress role is peripheral to RBOHD's central function in the immune ROS burst.
Supporting Evidence:
PMID:15923322
Mutations in nicotinamide adenine dinucleotide phosphate oxidase homolog genes (atrbohB and D) ... showed weaker defects
GO:0016174 NAD(P)H oxidase H2O2-forming activity
TAS
PMID:15608336
Cytosolic ascorbate peroxidase 1 is a central component of t...
MODIFY
Summary: As above, RBOHD is an NADPH oxidase; its primary product is superoxide, with H2O2 produced by dismutation. The superoxide-generating activity term (GO:0016175) is the more accurate molecular function.
Reason: Same rationale as the IMP-supported GO:0016174 annotation; the proximal reaction generates superoxide. Replace with the superoxide-generating NAD(P)H oxidase activity term.
Supporting Evidence:
PMID:11756663
O is the first ROI produced
GO:0006952 defense response
IMP
PMID:11756663
Arabidopsis gp91phox homologues AtrbohD and AtrbohF are requ...
ACCEPT
Summary: Loss of RBOHD eliminates most pathogen-induced ROS during incompatible (avirulent) interactions, establishing RBOHD as essential for the defense oxidative burst. This is a core biological process.
Reason: Strong genetic (IMP) support; defense response via the ROS burst is the central biological role of RBOHD.
Supporting Evidence:
PMID:11756663
AtrbohD and AtrbohF are required for accumulation of reactive oxygen intermediates in the plant defense response
GO:0002679 respiratory burst involved in defense response
IMP
PMID:11756663
Arabidopsis gp91phox homologues AtrbohD and AtrbohF are requ...
NEW
Summary: RBOHD is the principal enzyme producing the apoplastic oxidative ("respiratory") burst that accompanies plant immune responses; rbohD mutants lose most pathogen-induced extracellular ROS. This specific term captures the defining immune process better than the generic ROS metabolic process / defense response terms.
Reason: A more precise BP term (verified in GO as GO:0002679) directly describing the RBOHD-generated immune oxidative burst, supported by mutant genetics and by the activation of RBOHD within the FLS2/BIK1 PRR complex.
Supporting Evidence:
PMID:11756663
extracellular ROI production in Arabidopsis requires Atrboh function
PMID:24629339
directly phosphorylates the NADPH oxidase RbohD at specific sites in a calcium-independent manner to enhance ROS generation
file:ARATH/RBOHD/RBOHD-deep-research-falcon.md
major NADPH oxidase responsible for pathogen-triggered ROS
GO:0016175 superoxide-generating NAD(P)H oxidase activity
IDA
PMID:11756663
Arabidopsis gp91phox homologues AtrbohD and AtrbohF are requ...
NEW
Summary: RBOHD is a gp91phox-homologous NADPH oxidase that transfers electrons from cytosolic NADPH across the plasma membrane to O2, producing superoxide as the proximal product (subsequently dismutated to H2O2). This is the informative, product-specific catalytic molecular function and the core activity of the protein.
Reason: Captures the accurate catalytic activity of RBOHD (superoxide generation), replacing the less accurate H2O2-forming term and the spurious peroxidase term. Verified GO ID via OLS.
Supporting Evidence:
PMID:11756663
an NADPH oxidase subunit is required for ROI production confirms Doke's original suggestion that O is the first ROI produced
file:ARATH/RBOHD/RBOHD-deep-research-falcon.md
catalyzes **electron transfer from cytosolic NADPH to molecular oxygen (O2)** to generate **superoxide (O2•−)** in the **apoplast**, which can subsequently form **H2O2**

Core Functions

Calcium- and phosphorylation-regulated plasma-membrane NADPH oxidase that transfers electrons from cytosolic NADPH across the membrane to molecular oxygen, generating apoplastic superoxide (the proximal reactive oxygen species, which dismutates to hydrogen peroxide). This is the catalytic core function of RBOHD.

Supporting Evidence:
  • PMID:11756663
    an NADPH oxidase subunit is required for ROI production confirms Doke's original suggestion that O is the first ROI produced
  • PMID:11756663
    AtrbohD and AtrbohF are required for accumulation of reactive oxygen intermediates in the plant defense response
  • file:ARATH/RBOHD/RBOHD-deep-research-falcon.md
    catalyzes **electron transfer from cytosolic NADPH to molecular oxygen (O2)** to generate **superoxide (O2•−)** in the **apoplast**, which can subsequently form **H2O2**

Binds calcium through its two N-terminal EF-hand motifs, conferring calcium dependence on oxidase activation; together with phosphorylation by immune kinases (e.g. BIK1), calcium binding switches RBOHD into its ROS-producing state during pattern-triggered immunity.

Molecular Function:
calcium ion binding
Cellular Locations:
Supporting Evidence:
  • PMID:24629339
    Here we show that the receptor-like cytoplasmic kinase BIK1, a component of the FLS2 immune receptor complex, not only positively regulates flg22-triggered calcium influx but also directly phosphorylates the NADPH oxidase RbohD at specific sites in a calcium-independent manner to enhance ROS generation.
  • file:ARATH/RBOHD/RBOHD-deep-research-falcon.md
    RBOHD is activated by direct Ca2+ binding to EF-hands and by phosphorylation

As the principal generator of pathogen-induced extracellular reactive oxygen species, RBOHD drives the immune oxidative burst and modulates the spatial spread of hypersensitive programmed cell death during plant defense.

Supporting Evidence:
  • PMID:11756663
    The AtrbohD gene is required for most of the ROI observed after inoculation with avirulent Pst
  • PMID:16170317
    the subsequent oxidative burst can suppress cell death in cells surrounding sites of NADPH oxidase activation
  • file:ARATH/RBOHD/RBOHD-deep-research-falcon.md
    major NADPH oxidase responsible for pathogen-triggered ROS

References

file:ARATH/RBOHD/RBOHD-deep-research-falcon.md
Falcon (Edison Scientific) deep research report for RBOHD
Gene Ontology annotation through association of InterPro records with GO terms
Automatic assignment of GO terms using logical inference, based on on inter-ontology links
Electronic Gene Ontology annotations created by ARBA machine learning models
Combined Automated Annotation using Multiple IEA Methods
AtSubP analysis
Arabidopsis gp91phox homologues AtrbohD and AtrbohF are required for accumulation of reactive oxygen intermediates in the plant defense response.
  • "AtrbohD and AtrbohF are required for accumulation of reactive oxygen intermediates in the plant defense response"
  • "an NADPH oxidase subunit is required for ROI production confirms Doke's original suggestion that O is the first ROI produced"
Cytosolic ascorbate peroxidase 1 is a central component of the reactive oxygen gene network of Arabidopsis.
Different signaling and cell death roles of heterotrimeric G protein alpha and beta subunits in the Arabidopsis oxidative stress response to ozone.
Heat stress phenotypes of Arabidopsis mutants implicate multiple signaling pathways in the acquisition of thermotolerance.
  • "Mutations in nicotinamide adenine dinucleotide phosphate oxidase homolog genes (atrbohB and D) ... showed weaker defects"
Pathogen-induced, NADPH oxidase-derived reactive oxygen intermediates suppress spread of cell death in Arabidopsis thaliana.
  • "the subsequent oxidative burst can suppress cell death in cells surrounding sites of NADPH oxidase activation"
Dual roles of reactive oxygen species and NADPH oxidase RBOHD in an Arabidopsis-Alternaria pathosystem.
  • "Functional RBOHD causes marked extracellular hydrogen peroxide accumulation as well as cell death in distinct, single cells"
Calmodulin-dependent activation of MAP kinase for ROS homeostasis in Arabidopsis.
  • "The MPK8 pathway negatively regulates ROS accumulation through controlling expression of the Rboh D gene"
Osmosensitive changes of carbohydrate metabolism in response to cellulose biosynthesis inhibition.
  • "osmotic support does not suppress CBI-induced metabolic changes in seedlings impaired in ... reactive oxygen species production (respiratory burst oxidase homolog DF [rbohDF])"
Isolation and proteomic characterization of the Arabidopsis Golgi defines functional and novel components involved in plant cell wall biosynthesis.
Putative glycosyltransferases and other plant Golgi apparatus proteins are revealed by LOPIT proteomics.
The FLS2-associated kinase BIK1 directly phosphorylates the NADPH oxidase RbohD to control plant immunity.
  • "the receptor-like cytoplasmic kinase BIK1, a component of the FLS2 immune receptor complex, not only positively regulates flg22-triggered calcium influx but also directly phosphorylates the NADPH oxidase RbohD at specific sites in a calcium-independent manner to enhance ROS generation"
PBL13 Is a Serine/Threonine Protein Kinase That Negatively Regulates Arabidopsis Immune Responses.
  • "PBL13 is able to associate with the nicotinamide adenine dinucleotide phosphate, reduced oxidase RESPIRATORY BURST OXIDASE HOMOLOG PROTEIN D (RBOHD) by split-luciferase complementation assay, and this association is disrupted by flagellin treatment"
Arabidopsis HY1-Modulated Stomatal Movement: An Integrative Hub Is Functionally Associated with ABI4 in Dehydration-Induced ABA Responsiveness.
  • "the promotion of ABA-triggered up-regulation of RbohD abundance and reactive oxygen species (ROS) levels in the hy1 mutant was almost fully blocked by the mutation of ABI4"
Universal stress protein HRU1 mediates ROS homeostasis under anoxia.
  • "HRU1 interacts with proteins that induce ROS production, the GTPase ROP2 and the NADPH oxidase RbohD, pointing to the existence of a low-oxygen-specific mechanism for the modulation of ROS levels"
A Lectin Receptor-Like Kinase Mediates Pattern-Triggered Salicylic Acid Signaling.
  • "LecRK-IX.2 is capable of inducing RbohD phosphorylation, likely by recruiting calcium-dependent protein kinases to trigger ROS production in Arabidopsis"
Global Analysis of Membrane-associated Protein Oligomerization Using Protein Correlation Profiling.
Integrative Analysis from the Epigenome to Translatome Uncovers Patterns of Dominant Nuclear Regulation during Transient Stress.
UniProtKB:Q9FIJ0
UniProtKB RBOHD_ARATH (Q9FIJ0) Respiratory burst oxidase homolog protein D.
  • "Calcium-dependent NADPH oxidase that generates superoxide. Involved in the generation of reactive oxygen species (ROS) during incompatible interactions with pathogens, in response to pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) signaling and in UV-B and abscisic acid ROS-dependent signaling"

Suggested Questions for Experts

Q: Which kinase (BIK1, SIK1, CPKs, LecRK-IX.2) phosphorylation events are necessary versus sufficient for RBOHD activation in vivo, and how do they integrate with EF-hand calcium binding?

Q: To what extent is RBOHD a hub for the systemic ROS wave, and what determines cell-to-cell propagation of its activation across tissues?

Q: How do the recently described negative-regulatory and turnover mechanisms (PB1CP-mediated BIK1 displacement and endocytosis, PBL13/PIRE-mediated ubiquitination/vacuolar degradation, and CBE1-mediated translational repression of RBOHD accumulation) quantitatively shape the amplitude and transience of the immune ROS burst?

Deep Research

Falcon

(RBOHD-deep-research-falcon.md)
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate. Falcon Edison Scientific Literature 36 citations 2 artifacts 2026-06-06T22:01:53.744535

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Research report: Arabidopsis thaliana RBOHD (UniProt Q9FIJ0, locus At5g47910) — functional annotation and current understanding

1) Gene/protein identity verification (mandatory)

The target protein is Arabidopsis thaliana Respiratory burst oxidase homolog protein D (RBOHD; AtRBOHD), a member of the plant RBOH/NOX family of plasma-membrane NADPH oxidases that generate apoplastic reactive oxygen species (ROS). Multiple sources converge on the defining features expected from the UniProt entry: an N‑terminal regulatory region with EF‑hand Ca2+‑binding motifs, a C‑terminal catalytic core with FAD- and NADPH-binding regions, and a multi-pass membrane region with heme cofactors enabling electron transport across the membrane to reduce O2 to superoxide. (hasan2019theroleof pages 24-27, krainiukova2025regulationofplant pages 7-10, hu2020nadphoxidasesthe pages 3-5, zhang2023evolutionaryanalysisof pages 1-2, torres2024unveilingwhatmakes pages 2-2)

2) Key concepts and definitions (current understanding)

2.1 What is RBOHD?

RBOHD is a plant NADPH oxidase (also called an RBOH) that catalyzes electron transfer from cytosolic NADPH to molecular oxygen (O2) to generate superoxide (O2•−) in the apoplast, which can subsequently form H2O2 (spontaneously or via superoxide dismutase). (hasan2019theroleof pages 24-27, zhang2023evolutionaryanalysisof pages 1-2, torres2024unveilingwhatmakes pages 2-2)

2.2 Domain architecture and catalytic mechanism

RBOHD matches the canonical plant RBOH domain logic:
- N‑terminal cytosolic region with two EF‑hand Ca2+‑binding motifs and multiple regulatory phosphorylation sites; Ca2+ can directly stimulate activity via EF‑hands. (hasan2019theroleof pages 24-27, krainiukova2025regulationofplant pages 7-10, torres2024unveilingwhatmakes pages 2-2)
- C‑terminal cytosolic catalytic region containing FAD- and NADPH-binding domains, supporting electron flow from NADPH → FAD → hemes. (hasan2019theroleof pages 24-27, krainiukova2025regulationofplant pages 7-10, hu2020nadphoxidasesthe pages 3-5)
- Six transmembrane helices with two heme groups, with conserved histidines acting as axial ligands—consistent with intramembrane electron transfer. (hasan2019theroleof pages 24-27, krainiukova2025regulationofplant pages 7-10, zhang2023evolutionaryanalysisof pages 1-2)

These structural concepts explain how RBOHD can produce extracellular ROS while drawing reducing equivalents from the cytosolic NADPH pool. (krainiukova2025regulationofplant pages 7-10, zhang2023evolutionaryanalysisof pages 1-2)

2.3 “ROS burst” in plant immunity

A PAMP-triggered ROS burst is a rapid, transient increase in apoplastic ROS (often measured by luminol-based chemiluminescence) following recognition of pathogen-associated molecular patterns (PAMPs) by pattern recognition receptors (PRRs). Expert synthesis identifies RBOHD as the major NADPH oxidase responsible for pathogen-triggered ROS in Arabidopsis and highlights that its activity must be transient and tightly controlled to avoid damage. (torres2024unveilingwhatmakes pages 2-2)

3) Mechanistic regulation of RBOHD (with residue-level detail where available)

3.1 Calcium-dependent regulation

RBOHD can be activated directly by Ca2+ binding to its EF-hand motifs, and indirectly via Ca2+-dependent protein kinases (CPKs/CDPKs) that phosphorylate regulatory regions. (torres2024unveilingwhatmakes pages 2-2, krainiukova2025regulationofplant pages 7-10)

3.2 Phosphorylation sites and kinases (residue-level evidence)

A compilation source with residue mapping lists multiple phosphorylation sites on Arabidopsis RBOHD and associated kinases:
- DORN1S22, T24 (krainiukova2025regulationofplant pages 14-18)
- BIK1S39, S343, S347 (activation) (krainiukova2025regulationofplant pages 14-18)
- RIPKS343, S347 (krainiukova2025regulationofplant pages 14-18)
- MAP4KsS347 (krainiukova2025regulationofplant pages 14-18)
- CPK16S133, S148, S163, S347 (krainiukova2025regulationofplant pages 14-18)
- ALR1S39 (krainiukova2025regulationofplant pages 14-18)
- LKS4S39 on AtRBOHC/D/F (krainiukova2025regulationofplant pages 14-18)
Conserved/featured sites include S133, S163, S343, S347, T912 (with S39 moderately conserved and S148 weakly conserved in this summary). (krainiukova2025regulationofplant pages 14-18)

Expert commentary also highlights layered kinase control in immunity: BIK1/RIPK phosphorylation of N‑terminal residues and CRK2 phosphorylation of C‑terminal residues, with SIK1 acting directly or through BIK1. (torres2024unveilingwhatmakes pages 2-2)

3.3 Negative regulation, endocytosis, and turnover

Tight downregulation is a core principle: excessive ROS is detrimental, so plants employ both post-translational and post-transcriptional controls. (torres2024unveilingwhatmakes pages 2-2)

A 2024 primary study (New Phytologist) identifies PB1CP as a negative regulator of RBOHD:
- PB1CP was identified by co-immunoprecipitation + mass spectrometry as an RBOHD-associated factor. (goto2024thephagocytosisoxidasebem1p pages 1-2)
- PB1CP competes with BIK1 for binding to RBOHD in vitro; after PAMP treatment, PB1CP–RBOHD interaction increases and promotes dissociation of phosphorylated BIK1 from RBOHD in vivo. (goto2024thephagocytosisoxidasebem1p pages 1-2)
- PB1CP and RBOHD co-localize at the cell periphery and relocalize to small endomembrane compartments upon PAMP stimulation, consistent with a role in endocytosis. (goto2024thephagocytosisoxidasebem1p pages 1-2)
- PB1CP overexpression reduces RBOHD protein abundance, consistent with promoting removal/turnover. (goto2024thephagocytosisoxidasebem1p pages 1-2)

In a complementary expert synthesis focused on why the ROS burst is transient, additional deactivation layers are emphasized:
- PBL13 phosphorylates the RBOHD C‑terminus in the resting state and this promotes PIRE-mediated ubiquitination and vacuolar degradation.
- C‑terminal nitrosylation is described as a deactivation mechanism.
- PB1CP is framed as part of the endocytic/vacuolar downregulation pathway. (torres2024unveilingwhatmakes pages 2-2)

3.4 Post-transcriptional/translational control of RBOHD abundance (2023 primary study)

A 2023 Journal of Biological Chemistry study reports that CBE1 (MOB7; AT4G01290), an eIF4E1-binding protein associated with the 5′ mRNA cap and translation initiation machinery, negatively regulates accumulation of RBOHD protein. Loss/knockdown of CBE1 and related decapping/translation regulators leads to increased RBOHD abundance, elevated elicitor-induced apoplastic ROS, and enhanced antibacterial immunity—supporting a model in which RBOHD output is controlled at the level of translation/decapping-associated ribonucleoprotein regulation rather than only transcription. (george2023arabidopsistranslationinitiation pages 1-2)

4) Pathways and biological roles (where RBOHD acts)

4.1 Pattern-triggered immunity (PTI) and receptor-proximal signaling

In PTI, PRRs such as FLS2/EFR activate downstream cytoplasmic kinases (e.g., BIK1) that phosphorylate RBOHD to drive a rapid ROS burst. (goto2024theleucinerichrepeat pages 1-2)

A 2024 Plant Cell paper places RBOHD in a PRR-associated complex context by identifying QSK1, an LRR receptor kinase, as a PRR–RBOHD complex-associated negative regulator that downregulates PRR abundance (FLS2 and EFR), thereby dampening PTI; the bacterial effector HopF2Pto exploits QSK1 to suppress immunity. (goto2024theleucinerichrepeat pages 1-2)

4.2 Guard cell ABA signaling and stomatal closure

RBOHD (with RBOHF) is described as a pivotal ROS source for guard cell ABA signaling, supporting ABA-induced stomatal closure. (shen2020persulfidationbasedmodificationof pages 1-4)

In guard cells, redox post-translational modifications provide a mechanistic integration point: persulfidation of RBOHD at Cys825 and Cys890 enhances ROS production and is physiologically relevant to ABA-induced stomatal closure; the same Cys890 is also discussed as a site where S-nitrosylation can suppress ROS during defense. (shen2020persulfidationbasedmodificationof pages 1-4)

4.3 Abiotic stress, wound/damage signaling, and broader roles

A regulation-focused synthesis lists RBOHD involvement in diverse processes including wound-induced responses, damage-induced lignification, biotic and abiotic stress responses, and ABA-/JA-mediated stomatal closure (among others), consistent with its role as a major ROS-producing hub at the plasma membrane. (krainiukova2025regulationofplant pages 10-14)

A stress integration perspective similarly describes RBOHD as a major isoform active in both abiotic and biotic stress, producing apoplastic superoxide/H2O2 that can re-enter cells via aquaporins and function as a signal integrator across stress inputs. (kumar2025principlesofsignal pages 3-4)

5) Recent developments (prioritizing 2023–2024)

5.1 2023: Translational repression as an RBOHD control layer

The identification of CBE1 as a negative regulator of RBOHD protein accumulation adds a distinct “supply-side” mechanism controlling the amplitude of ROS bursts and immunity outcomes by modulating how much oxidase is available at baseline and/or after elicitation. (george2023arabidopsistranslationinitiation pages 1-2)

5.2 2024: Active downregulation mechanisms explaining burst transience

  • PB1CP: discovered as an RBOHD-binding factor that antagonizes BIK1 association and promotes endocytic relocalization/turnover, providing a mechanistic explanation for how plants terminate ROS production following activation. (goto2024thephagocytosisoxidasebem1p pages 1-2)
  • QSK1: positioned upstream by controlling PRR abundance in PRR–RBOHD complexes and exploited by HopF2Pto, clarifying how pathogens target the PRR→RBOHD axis. (goto2024theleucinerichrepeat pages 1-2)
  • Expert synthesis integrates these with PBL13/PIRE-mediated degradation and nitrosylation to frame RBOHD control as a multi-layer “on/off + removal” system. (torres2024unveilingwhatmakes pages 2-2)

6) Current applications and real-world implementations

Because RBOHD is a central hub for receptor-proximal ROS signaling across immunity and stress acclimation, it is widely discussed as a potential node for engineering stress resilience (e.g., tuning ROS amplitude/duration to improve disease resistance or abiotic stress tolerance), but with a key caveat: inappropriate ROS elevation can be detrimental, so strategies increasingly focus on regulatory modules (kinases/phosphatases, endocytosis/turnover factors, translation control) rather than constitutively increasing oxidase activity. This “tight-control” principle is explicitly emphasized in expert commentary regarding the need to avoid detrimental effects of ROS while enabling defense signaling. (torres2024unveilingwhatmakes pages 2-2, krainiukova2025regulationofplant pages 10-14)

7) Quantitative/statistical data available from the retrieved sources

Direct numeric effect sizes (e.g., fold-changes, kinetics parameters, pathogen growth values) were not present in the accessible text snippets. However, quantitative experimental outputs are available as figure evidence from the 2024 PB1CP paper:
- Luminol-based ROS burst assays show that pb1cp mutants display enhanced ROS bursts (triggered by flg22/elf18/chitin) whereas PB1CP overexpression reduces ROS bursts. (goto2024thephagocytosisoxidasebem1p media a584d7aa, goto2024thephagocytosisoxidasebem1p media 2bfdfcb1)
- An immunoblot shows reduced RBOHD protein abundance in PB1CP overexpression lines (basal and flg22-induced). (goto2024thephagocytosisoxidasebem1p media ed823380)

These figure-level data support the central quantitative claim that PB1CP modulates both ROS output and RBOHD protein abundance, even though the exact numeric values are not extractable from the current text-only snippets. (goto2024thephagocytosisoxidasebem1p media a584d7aa, goto2024thephagocytosisoxidasebem1p media ed823380)

8) Expert opinions and authoritative synthesis

Authoritative synthesis converges on a consensus model in which RBOHD serves as a receptor-proximal, plasma-membrane ROS generator whose activity integrates Ca2+ influx, kinase/phosphorylation circuits, and turnover/endocytosis to ensure ROS is produced with the correct magnitude and duration. This is clearly articulated in a 2024 expert commentary focused on why the immune ROS burst is transient, which highlights coordinated activation (EF-hands, BIK1/RIPK/CRK2/SIK1) and multiple shut-off/removal mechanisms (PBL13/PIRE ubiquitination, nitrosylation, PB1CP-mediated endocytosis). (torres2024unveilingwhatmakes pages 2-2)


Summary table

The following table consolidates key functional annotation points with the best supporting sources.

Functional aspect Key points Best supporting sources with year/venue and URL where available
Catalytic reaction Arabidopsis thaliana RBOHD (UniProt Q9FIJ0; At5g47910) is a canonical plant NADPH oxidase/RBOH that transfers electrons from cytosolic NADPH to molecular oxygen, producing apoplastic superoxide (O2•−), which then dismutates to H2O2 for signaling and defense. RBOHD is identified as the major generator of pathogen-triggered ROS in Arabidopsis. (hasan2019theroleof pages 24-27, zhang2023evolutionaryanalysisof pages 1-2, torres2024unveilingwhatmakes pages 2-2) Hasan 2019, review-like source/thesis (URL not available in snippet); Zhang et al. 2023, Int J Mol Sci https://doi.org/10.3390/ijms24043858; Torres 2024, New Phytologist https://doi.org/10.1111/nph.19502
Electron transfer cofactors/domains Defining RBOHD/RBOH architecture includes an extended cytosolic N-terminus with two EF-hand Ca2+-binding motifs and phosphorylation sites; a catalytic C-terminal core with FAD- and NADPH-binding domains; six transmembrane helices; and two heme groups coordinated by conserved His residues for electron transfer across the plasma membrane. These features align with the UniProt annotation and distinguish RBOHD from non-RBOH oxidoreductases such as FROs. (hasan2019theroleof pages 24-27, krainiukova2025regulationofplant pages 7-10, hu2020nadphoxidasesthe pages 3-5, zhang2023evolutionaryanalysisof pages 1-2, krainiukova2025regulationofplant pages 35-37) Hu et al. 2020, Cells https://doi.org/10.3390/cells9020437; Zhang et al. 2023, Int J Mol Sci https://doi.org/10.3390/ijms24043858; Hasan 2019, review-like source/thesis (URL not available in snippet)
Activation inputs: Ca2+ and phosphoregulation RBOHD is activated by direct Ca2+ binding to EF-hands and by phosphorylation. Residue-level sites supported in the available evidence: DORN1→S22/T24; BIK1→S39/S343/S347; RIPK→S343/S347; MAP4Ks→S347; CPK16→S133/S148/S163/S347; ALR1→S39; LKS4→S39 on AtRBOHC/D/F. Conserved phosphosites highlighted include S133, S163, S343, S347, and T912, with S39 moderately conserved and S148 weakly conserved. These modifications are linked to enzyme activation and ROS production. (krainiukova2025regulationofplantc pages 14-18, krainiukova2025regulationofplant pages 14-18, krainiukova2025regulationofplantd pages 14-18, krainiukova2025regulationofplanta pages 14-18) Krainiukova 2025, regulation review (journal not specified in snippet; URL not available); Torres 2024, New Phytologist https://doi.org/10.1111/nph.19502
PRR-linked activation and signaling complexes In PTI, PRR-BAK1 signaling activates BIK1, which phosphorylates RBOHD to trigger rapid ROS production. QSK1 is a PRR-RBOHD complex-associated LRR receptor kinase that downregulates FLS2 and EFR abundance and dampens PRR-triggered immunity. HopF2Pto exploits QSK1 to suppress this module. RBOHD therefore functions in a receptor-proximal signaling hub coupling PRRs to ROS and Ca2+ signaling. (goto2024theleucinerichrepeat pages 1-2, torres2024unveilingwhatmakes pages 2-2) Goto et al. 2024, Plant Cell https://doi.org/10.1093/plcell/koae267; Torres 2024, New Phytologist https://doi.org/10.1111/nph.19502
Negative regulation and turnover RBOHD is tightly downregulated to prevent excessive ROS. PB1CP is a 2024-defined negative regulator that binds RBOHD, competes with BIK1 for RBOHD association, enhances dissociation of phosphorylated BIK1 from RBOHD after PAMP treatment, and relocalizes with RBOHD to small endomembrane compartments, consistent with promotion of endocytosis. Overexpression of PB1CP lowers RBOHD protein abundance. Expert commentary further states that PBL13 phosphorylates the RBOHD C-terminus, promoting PIRE-mediated ubiquitination and vacuolar degradation; deactivation also involves C-terminal nitrosylation. (goto2024thephagocytosisoxidasebem1p pages 1-2, goto2024thephagocytosisoxidasebem1p pages 2-3, torres2024unveilingwhatmakes pages 2-2) Goto et al. 2024, New Phytologist https://doi.org/10.1111/nph.19302; Torres 2024, New Phytologist https://doi.org/10.1111/nph.19502
Post-transcriptional / translational control Beyond post-translational regulation, RBOHD abundance is controlled post-transcriptionally. George et al. identified CBE1, an eIF4E1-binding protein associated with the 5′ mRNA cap/translation initiation machinery, as a negative regulator of RBOHD accumulation. Loss or knockdown of CBE1 and related decapping/translation-initiation regulators increases RBOHD protein levels, enhances elicitor-induced apoplastic ROS, and increases antibacterial immunity, supporting translational control of RBOHD output. (george2023arabidopsistranslationinitiation pages 1-2) George et al. 2023, J Biol Chem https://doi.org/10.1016/j.jbc.2023.105018
Cellular localization RBOHD is a plasma membrane-localized NADPH oxidase that produces ROS into the apoplast. Its activity and spatial control are tied to membrane microdomains and receptor complexes at the cell periphery. Upon PAMP treatment, PB1CP and RBOHD relocalize from the cell periphery to small endomembrane compartments, consistent with regulated endocytosis/turnover. (hasan2019theroleof pages 24-27, krainiukova2025regulationofplant pages 35-37, goto2024thephagocytosisoxidasebem1p pages 1-2) Hasan 2019, review-like source/thesis (URL not available in snippet); Goto et al. 2024, New Phytologist https://doi.org/10.1111/nph.19302
Key biological processes Supported roles include pathogen-triggered immunity/PTI, fungal resistance, ROS-Ca2+ signal coupling, abiotic stress responses, wound/damage signaling, lignification, and ABA-/JA-related stomatal closure in broader RBOHD-focused regulation reviews/commentaries. In the supplied evidence, RBOHD is especially central to rapid PAMP-induced ROS production and downstream immune signaling. (krainiukova2025regulationofplant pages 10-14, torres2024unveilingwhatmakes pages 2-2, goto2024thephagocytosisoxidasebem1p pages 1-2, goto2024theleucinerichrepeat pages 1-2) Torres 2024, New Phytologist https://doi.org/10.1111/nph.19502; Goto et al. 2024, New Phytologist https://doi.org/10.1111/nph.19302; Goto et al. 2024, Plant Cell https://doi.org/10.1093/plcell/koae267
2023–2024 advances Notable recent advances in the supplied evidence are: (i) CBE1-mediated translational repression of RBOHD accumulation (2023); (ii) PB1CP as a negative regulator that removes phosphorylated BIK1 and promotes RBOHD endocytosis (2024); (iii) QSK1 as a PRR-RBOHD complex-associated regulator exploited by HopF2Pto (2024); and (iv) expert synthesis highlighting transient ROS burst control via PBL13/PIRE-mediated degradation, PB1CP action, and kinase layering (BIK1/RIPK/CRK2/SIK1). Direct quantitative fold-changes are not given in the available snippets, but the cited figures reportedly show enhanced ROS in pb1cp mutants, reduced ROS in PB1CP overexpressors, and reduced RBOHD protein abundance upon PB1CP overexpression. (goto2024thephagocytosisoxidasebem1p pages 1-2, goto2024theleucinerichrepeat pages 1-2, george2023arabidopsistranslationinitiation pages 1-2, torres2024unveilingwhatmakes pages 2-2, goto2024thephagocytosisoxidasebem1p media a584d7aa) George et al. 2023, J Biol Chem https://doi.org/10.1016/j.jbc.2023.105018; Goto et al. 2024, New Phytologist https://doi.org/10.1111/nph.19302; Goto et al. 2024, Plant Cell https://doi.org/10.1093/plcell/koae267; Torres 2024, New Phytologist https://doi.org/10.1111/nph.19502

Table: This table condenses the most relevant supported findings for Arabidopsis thaliana RBOHD, including catalytic function, domain architecture, residue-level regulation, localization, pathway context, and key 2023-2024 advances. It is useful as a citation-linked functional annotation snapshot restricted to claims supported by the provided evidence snippets.


Key primary references (2023–2024 prioritized; with dates and URLs)

  • George J. et al. (Aug 2023). Journal of Biological Chemistry. “CBE1 negatively regulates accumulation of the NADPH oxidase RBOHD.” https://doi.org/10.1016/j.jbc.2023.105018 (george2023arabidopsistranslationinitiation pages 1-2)
  • Goto Y. et al. (Oct 2024). The Plant Cell. “QSK1 regulates PRR–RBOHD complexes targeted by HopF2Pto.” https://doi.org/10.1093/plcell/koae267 (goto2024theleucinerichrepeat pages 1-2)
  • Goto Y. et al. (Oct 2024). New Phytologist. “PB1CP negatively regulates the NADPH oxidase RBOHD.” https://doi.org/10.1111/nph.19302 (goto2024thephagocytosisoxidasebem1p pages 1-2)
  • Torres M.-Á. (Jan 2024). New Phytologist (Commentary). “What makes the ROS burst transient: PB1CP in plant immunity.” https://doi.org/10.1111/nph.19502 (torres2024unveilingwhatmakes pages 2-2)

Supporting synthesis/seminal mechanistic reference

  • Shen J. et al. (Feb 2020). The Plant Cell. “Persulfidation-based modification of RBOHD controls guard cell ABA signaling.” https://doi.org/10.1105/tpc.19.00826 (shen2020persulfidationbasedmodificationof pages 1-4)
  • Zhang H. et al. (Feb 2023). International Journal of Molecular Sciences. “Evolutionary analysis of plant RBOHs; domain architecture and roles; Arabidopsis RBOHD/F in salt tolerance.” https://doi.org/10.3390/ijms24043858 (zhang2023evolutionaryanalysisof pages 1-2)
  • Hu C.-H. et al. (Feb 2020). Cells. “NADPH oxidases as central hubs in plant growth and signaling.” https://doi.org/10.3390/cells9020437 (hu2020nadphoxidasesthe pages 3-5)

Limitations of this report

This report is restricted to evidence retrievable in the current tool session. Some highly specific quantitative statistics (exact fold changes, kinetic parameters, pathogen growth CFU differences, precise PRR abundance changes) likely exist in the full primary papers but were not extractable from the available text snippets; where possible, figure-level evidence was retrieved to support quantitative claims (ROS burst and immunoblot changes in the PB1CP study). (goto2024thephagocytosisoxidasebem1p media a584d7aa, goto2024thephagocytosisoxidasebem1p media ed823380)

References

  1. (hasan2019theroleof pages 24-27): MS Hasan. The role of rboh-mediated ros and glutathione in plant-nematode interaction. Unknown journal, 2019.

  2. (krainiukova2025regulationofplant pages 7-10): E Krainiukova. Regulation of plant nadph oxidases: roles in development, cell polarity, and stress responses. Unknown journal, 2025.

  3. (hu2020nadphoxidasesthe pages 3-5): Chun-Hong Hu, Peng-Qi Wang, Peng-Peng Zhang, Xiu-Min Nie, Bin-Bin Li, Li Tai, Wen-Ting Liu, Wen-Qiang Li, and Kun-Ming Chen. Nadph oxidases: the vital performers and center hubs during plant growth and signaling. Cells, 9:437, Feb 2020. URL: https://doi.org/10.3390/cells9020437, doi:10.3390/cells9020437. This article has 187 citations.

  4. (zhang2023evolutionaryanalysisof pages 1-2): Haiyang Zhang, Xu Wang, An Yan, Jie Deng, Yanping Xie, Shiyuan Liu, Debin Liu, Lin He, Jianfeng Weng, and Jingyu Xu. Evolutionary analysis of respiratory burst oxidase homolog (rboh) genes in plants and characterization of zmrbohs. International Journal of Molecular Sciences, 24:3858, Feb 2023. URL: https://doi.org/10.3390/ijms24043858, doi:10.3390/ijms24043858. This article has 44 citations.

  5. (torres2024unveilingwhatmakes pages 2-2): Miguel‐Ángel Torres. Unveiling what makes the reactive oxygen species burst transient: the role of pb1cp in plant immunity. The New phytologist, 241:1384-1386, Jan 2024. URL: https://doi.org/10.1111/nph.19502, doi:10.1111/nph.19502. This article has 3 citations.

  6. (krainiukova2025regulationofplant pages 14-18): E Krainiukova. Regulation of plant nadph oxidases: roles in development, cell polarity, and stress responses. Unknown journal, 2025.

  7. (goto2024thephagocytosisoxidasebem1p pages 1-2): Yukihisa Goto, Noriko Maki, Jan Sklenar, Paul Derbyshire, Frank L. H. Menke, Cyril Zipfel, Yasuhiro Kadota, and Ken Shirasu. The phagocytosis oxidase/bem1p domain-containing protein pb1cp negatively regulates the nadph oxidase rbohd in plant immunity. The New phytologist, 241:1763-1779, Oct 2024. URL: https://doi.org/10.1111/nph.19302, doi:10.1111/nph.19302. This article has 20 citations.

  8. (george2023arabidopsistranslationinitiation pages 1-2): Jeoffrey George, Martin Stegmann, Jacqueline Monaghan, Julia Bailey-Serres, and Cyril Zipfel. Arabidopsis translation initiation factor binding protein cbe1 negatively regulates accumulation of the nadph oxidase respiratory burst oxidase homolog d. Journal of Biological Chemistry, 299:105018, Aug 2023. URL: https://doi.org/10.1016/j.jbc.2023.105018, doi:10.1016/j.jbc.2023.105018. This article has 10 citations and is from a domain leading peer-reviewed journal.

  9. (goto2024theleucinerichrepeat pages 1-2): Yukihisa Goto, Yasuhiro Kadota, Malick Mbengue, Jennifer D Lewis, Hidenori Matsui, Noriko Maki, Bruno Pok Man Ngou, Jan Sklenar, Paul Derbyshire, Arisa Shibata, Yasunori Ichihashi, David S Guttman, Hirofumi Nakagami, Takamasa Suzuki, Frank L H Menke, Silke Robatzek, Darrell Desveaux, Cyril Zipfel, and Ken Shirasu. The leucine-rich repeat receptor kinase qsk1 regulates prr-rbohd complexes targeted by the bacterial effector hopf2pto. The Plant Cell, 36:4932-4951, Oct 2024. URL: https://doi.org/10.1093/plcell/koae267, doi:10.1093/plcell/koae267. This article has 19 citations.

  10. (shen2020persulfidationbasedmodificationof pages 1-4): Jie Shen, Jing Zhang, Mingjian Zhou, Heng Zhou, Beimi Cui, Cecilia Gotor, Luis C. Romero, Ling Fu, Jing Yang, Christine Helen Foyer, Qiaona Pan, Wenbiao Shen, and Yanjie Xie. Persulfidation-based modification of cysteine desulfhydrase and the nadph oxidase rbohd controls guard cell abscisic acid signaling. Plant Cell, 32:1000-1017, Feb 2020. URL: https://doi.org/10.1105/tpc.19.00826, doi:10.1105/tpc.19.00826. This article has 295 citations and is from a highest quality peer-reviewed journal.

  11. (krainiukova2025regulationofplant pages 10-14): E Krainiukova. Regulation of plant nadph oxidases: roles in development, cell polarity, and stress responses. Unknown journal, 2025.

  12. (kumar2025principlesofsignal pages 3-4): Vijay Kumar, Madita Knieper, Lara Vogelsang, Ibadete Denjali, Thorsten Seidel, and Karl-Josef Dietz. Principles of signal integration in combinatorial stress acclimatization. Philosophical Transactions of the Royal Society B: Biological Sciences, May 2025. URL: https://doi.org/10.1098/rstb.2024.0243, doi:10.1098/rstb.2024.0243. This article has 2 citations and is from a domain leading peer-reviewed journal.

  13. (goto2024thephagocytosisoxidasebem1p media a584d7aa): Yukihisa Goto, Noriko Maki, Jan Sklenar, Paul Derbyshire, Frank L. H. Menke, Cyril Zipfel, Yasuhiro Kadota, and Ken Shirasu. The phagocytosis oxidase/bem1p domain-containing protein pb1cp negatively regulates the nadph oxidase rbohd in plant immunity. The New phytologist, 241:1763-1779, Oct 2024. URL: https://doi.org/10.1111/nph.19302, doi:10.1111/nph.19302. This article has 20 citations.

  14. (goto2024thephagocytosisoxidasebem1p media 2bfdfcb1): Yukihisa Goto, Noriko Maki, Jan Sklenar, Paul Derbyshire, Frank L. H. Menke, Cyril Zipfel, Yasuhiro Kadota, and Ken Shirasu. The phagocytosis oxidase/bem1p domain-containing protein pb1cp negatively regulates the nadph oxidase rbohd in plant immunity. The New phytologist, 241:1763-1779, Oct 2024. URL: https://doi.org/10.1111/nph.19302, doi:10.1111/nph.19302. This article has 20 citations.

  15. (goto2024thephagocytosisoxidasebem1p media ed823380): Yukihisa Goto, Noriko Maki, Jan Sklenar, Paul Derbyshire, Frank L. H. Menke, Cyril Zipfel, Yasuhiro Kadota, and Ken Shirasu. The phagocytosis oxidase/bem1p domain-containing protein pb1cp negatively regulates the nadph oxidase rbohd in plant immunity. The New phytologist, 241:1763-1779, Oct 2024. URL: https://doi.org/10.1111/nph.19302, doi:10.1111/nph.19302. This article has 20 citations.

  16. (krainiukova2025regulationofplant pages 35-37): E Krainiukova. Regulation of plant nadph oxidases: roles in development, cell polarity, and stress responses. Unknown journal, 2025.

  17. (krainiukova2025regulationofplantc pages 14-18): E Krainiukova. Regulation of plant nadph oxidases: roles in development, cell polarity, and stress responses. Unknown journal, 2025.

  18. (krainiukova2025regulationofplantd pages 14-18): E Krainiukova. Regulation of plant nadph oxidases: roles in development, cell polarity, and stress responses. Unknown journal, 2025.

  19. (krainiukova2025regulationofplanta pages 14-18): E Krainiukova. Regulation of plant nadph oxidases: roles in development, cell polarity, and stress responses. Unknown journal, 2025.

  20. (goto2024thephagocytosisoxidasebem1p pages 2-3): Yukihisa Goto, Noriko Maki, Jan Sklenar, Paul Derbyshire, Frank L. H. Menke, Cyril Zipfel, Yasuhiro Kadota, and Ken Shirasu. The phagocytosis oxidase/bem1p domain-containing protein pb1cp negatively regulates the nadph oxidase rbohd in plant immunity. The New phytologist, 241:1763-1779, Oct 2024. URL: https://doi.org/10.1111/nph.19302, doi:10.1111/nph.19302. This article has 20 citations.

Artifacts

Citations

  1. torres2024unveilingwhatmakes pages 2-2
  2. krainiukova2025regulationofplant pages 14-18
  3. george2023arabidopsistranslationinitiation pages 1-2
  4. goto2024theleucinerichrepeat pages 1-2
  5. shen2020persulfidationbasedmodificationof pages 1-4
  6. krainiukova2025regulationofplant pages 10-14
  7. kumar2025principlesofsignal pages 3-4
  8. zhang2023evolutionaryanalysisof pages 1-2
  9. hu2020nadphoxidasesthe pages 3-5
  10. hasan2019theroleof pages 24-27
  11. krainiukova2025regulationofplant pages 7-10
  12. krainiukova2025regulationofplant pages 35-37
  13. krainiukova2025regulationofplantc pages 14-18
  14. krainiukova2025regulationofplantd pages 14-18
  15. krainiukova2025regulationofplanta pages 14-18
  16. https://doi.org/10.3390/ijms24043858;
  17. https://doi.org/10.1111/nph.19502
  18. https://doi.org/10.3390/cells9020437;
  19. https://doi.org/10.1093/plcell/koae267;
  20. https://doi.org/10.1111/nph.19302;
  21. https://doi.org/10.1016/j.jbc.2023.105018
  22. https://doi.org/10.1111/nph.19302
  23. https://doi.org/10.1111/nph.19502;
  24. https://doi.org/10.1093/plcell/koae267
  25. https://doi.org/10.1016/j.jbc.2023.105018;
  26. https://doi.org/10.1105/tpc.19.00826
  27. https://doi.org/10.3390/ijms24043858
  28. https://doi.org/10.3390/cells9020437
  29. https://doi.org/10.3390/cells9020437,
  30. https://doi.org/10.3390/ijms24043858,
  31. https://doi.org/10.1111/nph.19502,
  32. https://doi.org/10.1111/nph.19302,
  33. https://doi.org/10.1016/j.jbc.2023.105018,
  34. https://doi.org/10.1093/plcell/koae267,
  35. https://doi.org/10.1105/tpc.19.00826,
  36. https://doi.org/10.1098/rstb.2024.0243,

📚 Additional Documentation

Notes

(RBOHD-notes.md)

RBOHD (Q9FIJ0) curation notes

Gene: RESPIRATORY BURST OXIDASE HOMOLOG PROTEIN D (RBOHD / AtrbohD), Arabidopsis thaliana, locus AT5G47910.

Identity and architecture (UniProt Q9FIJ0)

  • Plasma-membrane NADPH oxidase of the RBOH (TC 5.B.1.3) family; gp91phox/NOX homolog. 921 aa, six transmembrane helices, N-terminal cytoplasmic region (~1-376) carrying two canonical EF-hand Ca2+-binding domains (residues 253-288 and 297-332) plus EF-hand-like regions, and a C-terminal cytoplasmic FAD-binding (FR-type) + NADPH-binding ferredoxin-reductase module.
  • EC=1.6.3.- (NAD(P)H:oxygen oxidoreductase) and EC=1.11.1.- listed; BRENDA cross-reference 1.6.3.1.
  • Ca2+ binding sites at residues 266, 268, 270, 272, 277 (PROSITE EF-hand). [UniProt FT BINDING Ca(2+)]
  • Phosphoserines: Ser-8, Ser-9, Ser-26, Ser-39, Ser-339, Ser-343, Ser-347. Ser-39/Ser-343/Ser-347 phosphorylated by BIK1 upon flg22; Ser-347 (+Ser-8/9/339) by SIK1 — phosphorylation activates ROS production. [UniProt PTM]
  • UniProt FUNCTION: "Calcium-dependent NADPH oxidase that generates superoxide. Involved in the generation of reactive oxygen species (ROS) during incompatible interactions with pathogens, in response to pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) signaling and in UV-B and abscisic acid ROS-dependent signaling."
  • Subcellular location: Membrane; multi-pass membrane protein. Tissue: more abundant in roots; expressed in mesophyll and guard cells.

Core molecular function

RBOHD is the catalytic subunit of a plasma-membrane NADPH oxidase that transfers electrons from cytosolic NADPH across the membrane to molecular O2, producing apoplastic superoxide (O2.-), which dismutates to H2O2. The proximal product is superoxide:
- PMID:11756663
- The correct catalytic MF GO term is GO:0016175 "superoxide-generating NAD(P)H oxidase activity" (verified via OLS; def "NAD(P)H + O2 = NAD(P)+ + O2-"). The seeded annotations use GO:0016174 "NAD(P)H oxidase H2O2-forming activity" (def NAD(P)H + O2 = NAD(P)+ + H2O2) — H2O2 is formed only after dismutation of the primary superoxide product, so GO:0016175 is more accurate for RBOH proteins.

Activation / regulation

  • Calcium binds the EF-hands; activity is calcium-dependent (UniProt). GO:0005509 calcium ion binding is well supported by EF-hand domains.
  • BIK1, a receptor-like cytoplasmic kinase in the FLS2 complex, directly phosphorylates RBOHD at Ser-39/Ser-343/Ser-347 in a Ca2+-independent manner to enhance ROS. PMID:24629339
  • SIK1 (MAP4K) binds RBOHD upon flagellin perception and activates it by phosphorylation (Ser-347). [UniProt; PubMed:30212650]
  • PBL13 (a Ser/Thr RLCK) associates with RBOHD before pathogen perception and negatively regulates ROS; the association is disrupted by flg22. PMID:26432875
  • LecRK-IX.2 induces RBOHD phosphorylation, likely via CPKs, in pattern-triggered immunity. PMID:28696275
  • HRU1 (universal stress protein) interacts with RBOHD and ROP2 to modulate ROS under anoxia. PMID:27251529
  • MPK8 (Ca2+/CaM-MKK3 pathway) negatively regulates ROS via control of RbohD expression in wound signaling. PMID:21419340

Biological processes

  • PAMP/PTI immunity and the apoplastic oxidative (respiratory) burst; defense response. [PMID:11756663 "AtrbohD and AtrbohF are required for accumulation of reactive oxygen intermediates in the plant defense response"; "AtrbohD gene is required for most of the ROI observed after inoculation with avirulent Pst"]
  • Control/limitation of cell death: RBOHD-derived ROS suppress spread of hypersensitive cell death in surrounding cells (antagonize SA-dependent pro-death signals). PMID:16170317 Context-dependent (dual roles) in Alternaria pathosystem. PMID:19726575
  • Defense response to fungus (Alternaria brassicicola). PMID:19726575
  • ROS metabolic process / ROS gene network. [PMID:15608336; PMID:15705948 (ozone, G-protein)]
  • ABA/stomatal: RBOHD-derived ROS required for ABA-induced stomatal closure and drought responses. [PMID:26704641 "HY1-ABI4 signaling ... involved in stomatal closure was dependent on the RbohD-derived ROS production"; UniProt disruption phenotype "impaired in abscisic acid-induced stomatal closing"]
  • Osmosensing / carbohydrate homeostasis under cellulose-biosynthesis inhibition: rbohDF impaired in osmosensitive metabolic changes. PMID:22422940
  • Response to wounding (via MPK8 control of RbohD). PMID:21419340
  • Response to heat / thermotolerance: atrbohD shows weaker thermotolerance defects. PMID:15923322
  • Cellular response to hypoxia: RBOHD transcript regulation under transient hypoxia stress (HEP, translatome/epigenome study). PMID:31519798

Localization

  • Plasma membrane is the functional location (HDA proteomics PMID:22923678; abundant literature). Multi-pass PM protein.
  • Golgi (HDA, PMID:22430844 / LOPIT proteomics PMID:22923678) and plastid (HDA, PMID:28887381 protein-correlation profiling) signals are high-throughput organellar-proteomics assignments. For a multi-pass PM oxidase these most likely reflect endomembrane/secretory trafficking or co-fractionation rather than a distinct functional compartment; mark as over-annotated / non-core.
  • Nucleus (ISM, GO_REF:0000122, AtSubP prediction) is a computational subcellular-localization prediction with no experimental support for a nuclear RBOHD; a transmembrane PM oxidase is not expected in the nucleus. Remove.

GO term decisions summary

  • GO:0016175 superoxide-generating NAD(P)H oxidase activity = correct core MF (proposed replacement for GO:0016174).
  • GO:0005509 calcium ion binding = ACCEPT (EF-hands, Ca2+-dependent).
  • GO:0004601 peroxidase activity (IEA, InterPro/KW) = REMOVE/over-annotation: RBOHD is a superoxide-generating oxidase, not a peroxidase; the "Peroxidase" keyword derives from the gp91phox/cytochrome-b245 InterPro signature and is misleading.
  • GO:0016491 oxidoreductase, GO:0050664 oxidoreductase acting on NAD(P)H O2 acceptor = generic parents of GO:0016175; keep as accept (true but less informative).
  • GO:0098869 cellular oxidant detoxification (inferred from peroxidase activity) = REMOVE: RBOHD generates ROS for signaling, it does not detoxify oxidants; inference rests on the spurious peroxidase MF.
  • GO:0005515 protein binding (BIK1/FLS2, PBL13, HRU1, LecRK) = uninformative; mark over-annotated, captured better by molecular_function regulator interactions.
  • GO:0002679 respiratory burst involved in defense response = good candidate NEW BP term for the immune oxidative burst (verified via OLS).

Deep research synthesis (Falcon / Edison Scientific report)

Source: [file:ARATH/RBOHD/RBOHD-deep-research-falcon.md]. The Falcon deep research report corroborates and extends the existing review without contradicting any decisions.

  • Catalytic core confirmed: RBOHD "catalyzes electron transfer from cytosolic NADPH to molecular oxygen (O2) to generate superoxide (O2.-) in the apoplast, which can subsequently form H2O2" — reinforces GO:0016175 (superoxide-generating NAD(P)H oxidase) as the proximal-product MF over the H2O2-forming GO:0016174. Domain logic: N-terminal two EF-hand Ca2+-binding motifs, "a catalytic C-terminal core with FAD- and NADPH-binding domains", six TM helices with two hemes (His axial ligands).
  • Activation: "RBOHD is activated by direct Ca2+ binding to EF-hands and by phosphorylation" — supports GO:0005509 calcium ion binding as core. Residue-level phosphosites compiled: BIK1 -> S39/S343/S347; RIPK -> S343/S347; CPK16 -> S133/S148/S163/S347; SIK1/MAP4K -> S347; DORN1 -> S22/T24. PTI axis: "In PTI, PRRs such as FLS2/EFR activate downstream cytoplasmic kinases (e.g., BIK1) that phosphorylate RBOHD to drive a rapid ROS burst."
  • Immunity: RBOHD is the "major NADPH oxidase responsible for pathogen-triggered ROS" in Arabidopsis — supports GO:0006952 defense response and GO:0002679 respiratory burst involved in defense response as core.
  • Localization: "RBOHD is a plasma membrane-localized NADPH oxidase that produces ROS into the apoplast" — supports GO:0005886 plasma membrane as the functional compartment (consistent with marking Golgi/plastid/nucleus assignments as non-core/over-annotated/removed).
  • Guard-cell ABA signaling: RBOHD (with RBOHF) is "a pivotal ROS source for guard cell ABA signaling, supporting ABA-induced stomatal closure"; persulfidation at Cys825/Cys890 enhances ROS (Shen et al. 2020) — consistent with the ROS/stomatal-closure annotations.
  • New (2023-2024) negative regulators not in current GOA, captured as a suggested question rather than annotations: PB1CP (New Phytol 2024; competes with BIK1, promotes endocytosis/turnover, lowers RBOHD abundance); QSK1 (Plant Cell 2024; PRR-RBOHD complex-associated, downregulates FLS2/EFR, exploited by HopF2Pto); PBL13/PIRE ubiquitination + vacuolar degradation and C-terminal nitrosylation (Torres 2024 commentary); CBE1/MOB7 translational repression of RBOHD accumulation (JBC 2023). These provide mechanistic regulatory context; no new GO IDs were invented from them.

No annotation decisions were weakened. Falcon file: supporting_text entries were added to: GO:0005509 (Ca binding), GO:0006952 (defense, IEA), GO:0016491 (oxidoreductase), GO:0050664 (NAD(P)H O2-acceptor oxidoreductase), GO:0005886 (plasma membrane), GO:0005515 (BIK1/FLS2 interaction), GO:0002679 NEW, GO:0016175 NEW, and to the three core_functions.

📄 View Raw YAML

id: Q9FIJ0
gene_symbol: RBOHD
product_type: PROTEIN
status: DRAFT
taxon:
  id: NCBITaxon:3702
  label: Arabidopsis thaliana
description: >-
  RBOHD (Respiratory burst oxidase homolog protein D; AtrbohD) is a
  plasma-membrane, calcium-dependent NADPH oxidase of the RBOH/NOX (gp91phox
  homolog) family. The 921-residue, six-transmembrane protein carries an
  N-terminal cytoplasmic regulatory region with two EF-hand calcium-binding
  motifs and a C-terminal cytoplasmic FAD- and NADPH-binding ferredoxin
  reductase-like module. It transfers electrons from cytosolic NADPH across the
  plasma membrane to molecular oxygen, producing apoplastic superoxide that
  rapidly dismutates to hydrogen peroxide. RBOHD is the principal source of the
  extracellular oxidative ("respiratory") burst in plant immunity. Upon
  perception of pathogen-associated molecular patterns by surface receptors such
  as FLS2, it is activated by a rise in cytosolic calcium (via its EF-hands) and
  by phosphorylation by receptor-like cytoplasmic kinases (notably BIK1) and
  other kinases (SIK1, calcium-dependent protein kinases), while being held in
  check by negative regulators such as the kinase PBL13. The reactive oxygen
  species it produces act in PAMP-triggered immunity, in the regulation and
  spatial restriction of hypersensitive cell death, in long-distance ROS-wave
  systemic signaling, and in abscisic acid- and calcium-dependent stomatal
  closure. RBOHD also contributes ROS to abiotic stress responses including
  wounding, heat, UV-B, osmotic/cell-wall-integrity signaling, and low-oxygen
  stress. It is most abundant in roots and is expressed in mesophyll and guard
  cells.
existing_annotations:
- term:
    id: GO:0004601
    label: peroxidase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: RBOHD is a superoxide-generating NADPH oxidase, not a peroxidase.
      This IEA derives from the gp91phox/cytochrome-b245 (Cyt_b245) InterPro
      signature (IPR013623) and the associated UniProt "Peroxidase" keyword,
      which is misleading for RBOH proteins. The enzyme reduces O2 to
      superoxide using electrons from NADPH; it does not reduce hydrogen
      peroxide.
    action: REMOVE
    reason: The catalytic activity of RBOHD is electron transfer from NADPH to
      O2 to generate superoxide (and downstream H2O2 by dismutation), not
      peroxidase activity. The InterPro-derived peroxidase keyword is a known
      mis-mapping for the gp91phox family and over-annotates the gene. The
      informative catalytic term is GO:0016175 (added as NEW).
    supported_by:
    - reference_id: PMID:11756663
      supporting_text: our demonstration that an NADPH oxidase subunit is
        required for ROI production confirms Doke's original suggestion that
        O is the first ROI produced
- term:
    id: GO:0005509
    label: calcium ion binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: RBOHD contains two canonical N-terminal EF-hand calcium-binding
      domains (UniProt residues 253-288 and 297-332, with Ca2+ coordinated by
      residues 266/268/270/272/277) and is a calcium-dependent NADPH oxidase.
      Calcium binding to these EF-hands is integral to its activation.
    action: ACCEPT
    reason: Well supported by conserved EF-hand domains/Ca2+ binding sites in
      UniProt and by the calcium-dependence of RBOH oxidase activity. This is a
      core molecular function contributing to activity regulation.
    supported_by:
    - reference_id: PMID:24629339
      supporting_text: >-
        Here we show that the receptor-like cytoplasmic kinase BIK1, a component of the FLS2
        immune receptor complex, not only positively regulates flg22-triggered calcium influx
        but also directly phosphorylates the NADPH oxidase RbohD at specific sites in a
        calcium-independent manner to enhance ROS generation.
    - reference_id: file:ARATH/RBOHD/RBOHD-deep-research-falcon.md
      supporting_text: RBOHD is activated by direct Ca2+ binding to EF-hands and
        by phosphorylation
- term:
    id: GO:0006952
    label: defense response
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: involved_in
  review:
    summary: RBOHD generates the apoplastic ROS burst central to plant immune
      responses; rbohD mutants fail to accumulate ROS during pathogen defense.
      This electronic annotation is consistent with strong experimental
      evidence (see also the IMP defense response annotation below).
    action: ACCEPT
    reason: Defense response is a well-established core biological process for
      RBOHD, supported by mutant phenotypes during pathogen interactions.
    supported_by:
    - reference_id: PMID:11756663
      supporting_text: AtrbohD and AtrbohF are required for accumulation of
        reactive oxygen intermediates in the plant defense response
    - reference_id: file:ARATH/RBOHD/RBOHD-deep-research-falcon.md
      supporting_text: major NADPH oxidase responsible for pathogen-triggered ROS
- term:
    id: GO:0016020
    label: membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: located_in
  review:
    summary: RBOHD is a multi-pass (six transmembrane helix) integral membrane
      protein, specifically of the plasma membrane. This generic membrane term
      is correct but less informative than the plasma membrane annotation.
    action: ACCEPT
    reason: True location but generic; the more specific plasma membrane
      annotation (GO:0005886) captures the functional compartment. Retained as
      accurate but non-core relative to plasma membrane.
    supported_by:
    - reference_id: PMID:24629339
      supporting_text: directly phosphorylates the NADPH oxidase RbohD
- term:
    id: GO:0016491
    label: oxidoreductase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: RBOHD is an oxidoreductase that transfers electrons from NADPH to
      O2. This is a very general parent of the specific superoxide-generating
      NADPH oxidase activity.
    action: ACCEPT
    reason: Correct but high-level; acceptable as a broad IEA parent of the
      informative term GO:0016175. Not the core descriptor on its own.
    supported_by:
    - reference_id: PMID:11756663
      supporting_text: AtrbohD and AtrbohF, encoding probable components of a
        plant NADPH oxidase
    - reference_id: file:ARATH/RBOHD/RBOHD-deep-research-falcon.md
      supporting_text: catalyzes **electron transfer from cytosolic NADPH to
        molecular oxygen (O2)** to generate **superoxide (O2•−)** in the
        **apoplast**, which can subsequently form **H2O2**
- term:
    id: GO:0050664
    label: oxidoreductase activity, acting on NAD(P)H, oxygen as acceptor
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: This term correctly describes RBOHD as an NAD(P)H-dependent
      oxidoreductase using oxygen as electron acceptor, which is precisely the
      RBOH oxidase chemistry. It is the immediate parent of the
      superoxide-generating term GO:0016175.
    action: ACCEPT
    reason: Accurate and reasonably specific; consistent with the NADPH-binding
      ferredoxin-reductase module and O2-reducing oxidase activity. The
      product-specific child term GO:0016175 is added as NEW.
    supported_by:
    - reference_id: PMID:11756663
      supporting_text: an NADPH oxidase subunit is required for ROI production
    - reference_id: file:ARATH/RBOHD/RBOHD-deep-research-falcon.md
      supporting_text: a catalytic C-terminal core with FAD- and NADPH-binding
        domains
- term:
    id: GO:0098869
    label: cellular oxidant detoxification
  evidence_type: IEA
  original_reference_id: GO_REF:0000108
  qualifier: involved_in
  review:
    summary: This term is inferred logically from the spurious peroxidase MF
      (GO:0004601 to GO:0098869). RBOHD generates reactive oxygen species for
      signaling; it does not detoxify cellular oxidants. The annotation is
      essentially backwards with respect to the protein's biology.
    action: REMOVE
    reason: RBOHD is a ROS-producing enzyme, not an antioxidant/detoxifying
      enzyme. The inference depends on the incorrect peroxidase activity
      assignment, which is itself being removed.
    supported_by:
    - reference_id: PMID:19726575
      supporting_text: Functional RBOHD causes marked extracellular hydrogen
        peroxide accumulation
- term:
    id: GO:0005794
    label: Golgi apparatus
  evidence_type: HDA
  original_reference_id: PMID:22430844
  qualifier: located_in
  review:
    summary: A Golgi assignment from high-throughput organellar proteomics. For
      a multi-pass plasma-membrane oxidase, a Golgi signal most plausibly
      reflects transit through the secretory pathway or co-fractionation rather
      than a functional Golgi pool. The functional location is the plasma
      membrane.
    action: MARK_AS_OVER_ANNOTATED
    reason: High-throughput proteomic localization without functional support;
      inconsistent with the established plasma-membrane site of RBOHD action.
      Likely reflects biosynthetic trafficking or proteomic co-fractionation.
    supported_by:
    - reference_id: PMID:22430844
      supporting_text: Isolation and proteomic characterization of the
        Arabidopsis Golgi
- term:
    id: GO:0005886
    label: plasma membrane
  evidence_type: HDA
  original_reference_id: PMID:22923678
  qualifier: located_in
  review:
    summary: The plasma membrane is the functional location of RBOHD. It is a
      multi-pass plasma-membrane NADPH oxidase that releases superoxide into the
      apoplast, where it acts together with plasma-membrane receptor complexes
      (FLS2/BIK1) in immune signaling.
    action: ACCEPT
    reason: Strongly supported by proteomics and by the abundant literature
      placing RBOHD in plasma-membrane PRR complexes; this is the core cellular
      location for its function.
    supported_by:
    - reference_id: PMID:24629339
      supporting_text: BIK1, a component of the FLS2 immune receptor complex
    - reference_id: PMID:22923678
      supporting_text: plant Golgi apparatus proteins are revealed by LOPIT
        proteomics
    - reference_id: file:ARATH/RBOHD/RBOHD-deep-research-falcon.md
      supporting_text: RBOHD is a plasma membrane-localized NADPH oxidase that
        produces ROS into the apoplast
- term:
    id: GO:0071456
    label: cellular response to hypoxia
  evidence_type: HEP
  original_reference_id: PMID:31519798
  qualifier: acts_upstream_of_or_within
  review:
    summary: RBOHD expression/regulation is captured in an integrative
      epigenome-to-translatome study of transient stress that includes hypoxia.
      Consistent with a role for RBOH-derived ROS in low-oxygen responses (cf.
      HRU1/ROP2/RbohD module under anoxia), this peripheral, expression-pattern
      based annotation is plausible but not a core function.
    action: KEEP_AS_NON_CORE
    reason: Expression-pattern (HEP) evidence from a high-throughput stress
      study; supports involvement in hypoxia responses but as a peripheral
      process rather than a defining function. Concordant with independent
      anoxia evidence (PMID:27251529).
    supported_by:
    - reference_id: PMID:27251529
      supporting_text: HRU1 interacts with proteins that induce ROS production,
        the GTPase ROP2 and the NADPH oxidase RbohD, pointing to the existence
        of a low-oxygen-specific mechanism for the modulation of ROS levels
- term:
    id: GO:0009536
    label: plastid
  evidence_type: HDA
  original_reference_id: PMID:28887381
  qualifier: located_in
  review:
    summary: A plastid assignment from a global membrane-protein
      correlation-profiling study. RBOHD is a plasma-membrane oxidase; a
      plastid location is not supported by any functional study and most likely
      reflects co-fractionation/contamination in the high-throughput dataset.
    action: REMOVE
    reason: No functional or targeted experimental support for a plastid pool of
      RBOHD; inconsistent with its plasma-membrane topology and apoplastic ROS
      output. Likely a proteomic artifact.
    supported_by:
    - reference_id: PMID:28887381
      supporting_text: Global Analysis of Membrane-associated Protein
        Oligomerization Using Protein Correlation Profiling
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: ISM
  original_reference_id: GO_REF:0000122
  qualifier: located_in
  review:
    summary: A purely computational subcellular-localization prediction (AtSubP).
      A six-transmembrane plasma-membrane oxidase is not expected to localize to
      the nucleus, and no experimental evidence supports a nuclear RBOHD.
    action: REMOVE
    reason: Sequence-based prediction (ISM) contradicted by the membrane
      topology and experimentally established plasma-membrane localization. No
      supporting functional evidence.
    supported_by:
    - reference_id: PMID:22923678
      supporting_text: plant Golgi apparatus proteins are revealed by LOPIT
        proteomics
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:28696275
  qualifier: enables
  review:
    summary: Refers to functional interaction within pattern-triggered immunity
      signaling; the lectin receptor-like kinase LecRK-IX.2 induces RBOHD
      phosphorylation (likely via calcium-dependent protein kinases) to trigger
      ROS. "Protein binding" is uninformative about RBOHD's actual molecular
      function.
    action: MARK_AS_OVER_ANNOTATED
    reason: Generic protein binding conveys no specific functional information.
      The biologically meaningful content (regulation of RBOHD ROS output by
      upstream immune kinases) is captured in the core_functions and process
      annotations rather than by GO:0005515.
    supported_by:
    - reference_id: PMID:28696275
      supporting_text: LecRK-IX.2 is capable of inducing RbohD phosphorylation,
        likely by recruiting calcium-dependent protein kinases to trigger ROS
        production in Arabidopsis
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:24629339
  qualifier: enables
  review:
    summary: This IPI records the interaction of RBOHD with BIK1 and FLS2. BIK1
      directly phosphorylates RBOHD to enhance ROS during immunity. While
      biologically important, the bare "protein binding" term is uninformative.
    action: MARK_AS_OVER_ANNOTATED
    reason: The interaction with BIK1/FLS2 is a key activation mechanism, but
      GO:0005515 does not capture it usefully. The functional relationship
      (kinase-mediated activation of RBOHD) is documented in notes and
      core_functions; a specific kinase-binding term would be preferable but is
      not added here to avoid over-fitting.
    supported_by:
    - reference_id: PMID:24629339
      supporting_text: the receptor-like cytoplasmic kinase BIK1, a component of
        the FLS2 immune receptor complex ... directly phosphorylates the NADPH
        oxidase RbohD at specific sites
    - reference_id: file:ARATH/RBOHD/RBOHD-deep-research-falcon.md
      supporting_text: In PTI, PRRs such as FLS2/EFR activate downstream
        cytoplasmic kinases (e.g., BIK1) that phosphorylate RBOHD to drive a
        rapid ROS burst
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:26432875
  qualifier: enables
  review:
    summary: Records the interaction of RBOHD with the negative-regulatory
      kinase PBL13 (split-luciferase complementation), which is disrupted by
      flagellin treatment. Informative biologically but not captured by the
      generic term.
    action: MARK_AS_OVER_ANNOTATED
    reason: Generic protein binding is uninformative. The PBL13 interaction is a
      negative-regulatory mechanism for RBOHD ROS production, documented in
      notes; GO:0005515 itself should not be treated as a core molecular
      function.
    supported_by:
    - reference_id: PMID:26432875
      supporting_text: PBL13 is able to associate with the nicotinamide adenine
        dinucleotide phosphate, reduced oxidase RESPIRATORY BURST OXIDASE
        HOMOLOG PROTEIN D (RBOHD) by split-luciferase complementation assay,
        and this association is disrupted by flagellin treatment
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:27251529
  qualifier: enables
  review:
    summary: Records interaction of RBOHD with the universal stress protein HRU1
      (and ROP2) in modulating ROS production under anoxia. Biologically
      meaningful but uninformative as a bare protein-binding term.
    action: MARK_AS_OVER_ANNOTATED
    reason: Generic protein binding lacks specificity. The HRU1/ROP2 interaction
      links oxygen sensing to RBOHD ROS output under low oxygen; documented in
      notes rather than via GO:0005515.
    supported_by:
    - reference_id: PMID:27251529
      supporting_text: HRU1 interacts with proteins that induce ROS production,
        the GTPase ROP2 and the NADPH oxidase RbohD
- term:
    id: GO:0072593
    label: reactive oxygen species metabolic process
  evidence_type: IGI
  original_reference_id: PMID:26704641
  qualifier: acts_upstream_of_or_within
  review:
    summary: RBOHD-derived ROS are required for ABA/HY1-ABI4-dependent stomatal
      closure; genetic interaction places RBOHD upstream of the ROS levels that
      mediate stomatal movement. Consistent with RBOHD as a primary ROS
      generator.
    action: ACCEPT
    reason: Well supported; RBOHD is a major contributor to cellular ROS
      metabolism, here in the context of ABA-dependent stomatal regulation.
    supported_by:
    - reference_id: PMID:26704641
      supporting_text: the promotion of ABA-triggered up-regulation of RbohD
        abundance and reactive oxygen species (ROS) levels in the hy1 mutant
        was almost fully blocked by the mutation of ABI4
- term:
    id: GO:0007231
    label: osmosensory signaling pathway
  evidence_type: IMP
  original_reference_id: PMID:22422940
  qualifier: acts_upstream_of_or_within
  review:
    summary: In cellulose-biosynthesis-inhibition experiments, rbohDF mutants
      fail to show the osmosensitive metabolic changes, implicating
      RBOHD/F-derived ROS in osmo/cell-wall-integrity signaling.
    action: KEEP_AS_NON_CORE
    reason: Supported by mutant phenotype, but this is a specialized,
      peripheral signaling context relative to RBOHD's central immune/ROS-burst
      role. Retained as a genuine but non-core process.
    supported_by:
    - reference_id: PMID:22422940
      supporting_text: osmotic support does not suppress CBI-induced metabolic
        changes in seedlings impaired in ... reactive oxygen species production
        (respiratory burst oxidase homolog DF [rbohDF])
- term:
    id: GO:0033500
    label: carbohydrate homeostasis
  evidence_type: IMP
  original_reference_id: PMID:22422940
  qualifier: acts_upstream_of_or_within
  review:
    summary: The same study links RBOHD/F-derived ROS to osmosensitive control
      of carbohydrate metabolism after cellulose biosynthesis inhibition. The
      effect on carbohydrate homeostasis is indirect and downstream of the
      osmo-signaling role.
    action: KEEP_AS_NON_CORE
    reason: Indirect, context-specific phenotype; ROS from RBOHD feed into an
      osmosensitive regulatory circuit that affects carbohydrate metabolism, but
      this is peripheral to the protein's core ROS-generating immune function.
    supported_by:
    - reference_id: PMID:22422940
      supporting_text: carbohydrate metabolism is responsive to changes in
        cellulose biosynthesis activity and turgor pressure
- term:
    id: GO:0009611
    label: response to wounding
  evidence_type: IEP
  original_reference_id: PMID:21419340
  qualifier: acts_upstream_of_or_within
  review:
    summary: The Ca2+/CaM-MPK8-MKK3 wound-signaling pathway negatively regulates
      ROS accumulation through control of RbohD expression, linking RBOHD to
      wound-induced ROS homeostasis.
    action: KEEP_AS_NON_CORE
    reason: RBOHD participates in wound-induced ROS homeostasis (as a regulated
      ROS source), but the evidence is expression-pattern based (IEP) and the
      process is peripheral to its central immune ROS-burst function.
    supported_by:
    - reference_id: PMID:21419340
      supporting_text: The MPK8 pathway negatively regulates ROS accumulation
        through controlling expression of the Rboh D gene
- term:
    id: GO:0072593
    label: reactive oxygen species metabolic process
  evidence_type: IMP
  original_reference_id: PMID:11756663
  qualifier: acts_upstream_of_or_within
  review:
    summary: rbohD insertion mutants eliminate the majority of pathogen-induced
      ROS, demonstrating that RBOHD is the principal generator of the defense
      oxidative burst. This is a core process annotation.
    action: ACCEPT
    reason: Strong genetic evidence that RBOHD drives ROS metabolic process
      (the extracellular oxidative burst) during defense; a defining function.
    supported_by:
    - reference_id: PMID:11756663
      supporting_text: The AtrbohD gene is required for most of the ROI observed
        after inoculation with avirulent Pst
- term:
    id: GO:0072593
    label: reactive oxygen species metabolic process
  evidence_type: TAS
  original_reference_id: PMID:15705948
  qualifier: acts_upstream_of_or_within
  review:
    summary: RBOHD is part of the Arabidopsis ROS gene network and contributes
      ROS in the oxidative stress response (including ozone/G-protein-mediated
      responses). Consistent with its established role in ROS production.
    action: ACCEPT
    reason: TAS annotation consistent with the well-documented role of RBOHD as
      a generator of signaling ROS; duplicate aspect of the core ROS metabolic
      process annotation.
    supported_by:
    - reference_id: PMID:11756663
      supporting_text: extracellular ROI production in Arabidopsis requires
        Atrboh function
- term:
    id: GO:0043069
    label: negative regulation of programmed cell death
  evidence_type: IGI
  original_reference_id: PMID:16170317
  qualifier: acts_upstream_of_or_within
  review:
    summary: RBOHD-derived ROS suppress the spread of hypersensitive cell death
      into cells surrounding infection sites, antagonizing salicylic
      acid-dependent pro-death signals. Thus RBOHD limits cell-death spread even
      though its ROS can also trigger localized death.
    action: ACCEPT
    reason: Supported by genetic evidence; an established (if context-dependent)
      role of RBOHD in restricting programmed cell death spread during the
      immune response.
    supported_by:
    - reference_id: PMID:16170317
      supporting_text: the subsequent oxidative burst can suppress cell death in
        cells surrounding sites of NADPH oxidase activation
    - reference_id: PMID:19726575
      supporting_text: functional RBOHD triggers death in cells that are damaged
        by fungal infection but simultaneously inhibits death in neighboring
        cells
- term:
    id: GO:0016174
    label: NAD(P)H oxidase H2O2-forming activity
  evidence_type: IMP
  original_reference_id: PMID:19726575
  qualifier: enables
  review:
    summary: RBOHD is a NADPH oxidase whose immediate enzymatic product is
      superoxide; the measured apoplastic H2O2 arises by (spontaneous or
      SOD-catalyzed) dismutation of that superoxide. The more accurate catalytic
      term is GO:0016175 "superoxide-generating NAD(P)H oxidase activity". The
      H2O2-forming term reflects the downstream detected species rather than the
      primary reaction.
    action: MODIFY
    reason: The proximal product is superoxide (PMID:11756663), so the
      product-specific MF should be the superoxide-generating activity. H2O2 is
      formed secondarily by dismutation, making GO:0016174 a less accurate
      descriptor of the catalyzed reaction.
    proposed_replacement_terms:
    - id: GO:0016175
      label: superoxide-generating NAD(P)H oxidase activity
    supported_by:
    - reference_id: PMID:11756663
      supporting_text: O is the first ROI produced
    - reference_id: PMID:19726575
      supporting_text: Functional RBOHD causes marked extracellular hydrogen
        peroxide accumulation
- term:
    id: GO:0050832
    label: defense response to fungus
  evidence_type: IMP
  original_reference_id: PMID:19726575
  qualifier: acts_upstream_of_or_within
  review:
    summary: rbohD knockout alters ROS accumulation and cell-death patterns upon
      infection with the necrotrophic fungus Alternaria brassicicola,
      demonstrating involvement in antifungal defense (with dual, position-
      dependent effects on cell death).
    action: ACCEPT
    reason: Supported by mutant phenotype in a defined fungal pathosystem; a
      genuine, if context-dependent, defense-against-fungus role for RBOHD.
    supported_by:
    - reference_id: PMID:19726575
      supporting_text: a rbohD knockout mutant exhibits increased spread of cell
        death at the macroscopic level upon inoculation with the fungus
        Alternaria brassicicola
- term:
    id: GO:0009408
    label: response to heat
  evidence_type: IMP
  original_reference_id: PMID:15923322
  qualifier: acts_upstream_of_or_within
  review:
    summary: atrbohD mutants show (weaker) defects in acquired thermotolerance,
      implicating RBOHD-derived ROS/oxidative-burst signaling in the heat-stress
      response among multiple contributing pathways.
    action: KEEP_AS_NON_CORE
    reason: Supported by mutant phenotype but the effect is relatively weak and
      this abiotic-stress role is peripheral to RBOHD's central function in the
      immune ROS burst.
    supported_by:
    - reference_id: PMID:15923322
      supporting_text: Mutations in nicotinamide adenine dinucleotide phosphate
        oxidase homolog genes (atrbohB and D) ... showed weaker defects
- term:
    id: GO:0016174
    label: NAD(P)H oxidase H2O2-forming activity
  evidence_type: TAS
  original_reference_id: PMID:15608336
  qualifier: enables
  review:
    summary: As above, RBOHD is an NADPH oxidase; its primary product is
      superoxide, with H2O2 produced by dismutation. The superoxide-generating
      activity term (GO:0016175) is the more accurate molecular function.
    action: MODIFY
    reason: Same rationale as the IMP-supported GO:0016174 annotation; the
      proximal reaction generates superoxide. Replace with the
      superoxide-generating NAD(P)H oxidase activity term.
    proposed_replacement_terms:
    - id: GO:0016175
      label: superoxide-generating NAD(P)H oxidase activity
    supported_by:
    - reference_id: PMID:11756663
      supporting_text: O is the first ROI produced
- term:
    id: GO:0006952
    label: defense response
  evidence_type: IMP
  original_reference_id: PMID:11756663
  qualifier: acts_upstream_of_or_within
  review:
    summary: Loss of RBOHD eliminates most pathogen-induced ROS during
      incompatible (avirulent) interactions, establishing RBOHD as essential for
      the defense oxidative burst. This is a core biological process.
    action: ACCEPT
    reason: Strong genetic (IMP) support; defense response via the ROS burst is
      the central biological role of RBOHD.
    supported_by:
    - reference_id: PMID:11756663
      supporting_text: AtrbohD and AtrbohF are required for accumulation of
        reactive oxygen intermediates in the plant defense response
- term:
    id: GO:0002679
    label: respiratory burst involved in defense response
  evidence_type: IMP
  original_reference_id: PMID:11756663
  qualifier: involved_in
  review:
    summary: RBOHD is the principal enzyme producing the apoplastic oxidative
      ("respiratory") burst that accompanies plant immune responses; rbohD
      mutants lose most pathogen-induced extracellular ROS. This specific term
      captures the defining immune process better than the generic ROS metabolic
      process / defense response terms.
    action: NEW
    reason: A more precise BP term (verified in GO as GO:0002679) directly
      describing the RBOHD-generated immune oxidative burst, supported by mutant
      genetics and by the activation of RBOHD within the FLS2/BIK1 PRR complex.
    supported_by:
    - reference_id: PMID:11756663
      supporting_text: extracellular ROI production in Arabidopsis requires
        Atrboh function
    - reference_id: PMID:24629339
      supporting_text: directly phosphorylates the NADPH oxidase RbohD at
        specific sites in a calcium-independent manner to enhance ROS generation
    - reference_id: file:ARATH/RBOHD/RBOHD-deep-research-falcon.md
      supporting_text: major NADPH oxidase responsible for pathogen-triggered ROS
- term:
    id: GO:0016175
    label: superoxide-generating NAD(P)H oxidase activity
  evidence_type: IDA
  original_reference_id: PMID:11756663
  qualifier: enables
  review:
    summary: RBOHD is a gp91phox-homologous NADPH oxidase that transfers
      electrons from cytosolic NADPH across the plasma membrane to O2, producing
      superoxide as the proximal product (subsequently dismutated to H2O2). This
      is the informative, product-specific catalytic molecular function and the
      core activity of the protein.
    action: NEW
    reason: Captures the accurate catalytic activity of RBOHD (superoxide
      generation), replacing the less accurate H2O2-forming term and the
      spurious peroxidase term. Verified GO ID via OLS.
    supported_by:
    - reference_id: PMID:11756663
      supporting_text: an NADPH oxidase subunit is required for ROI production
        confirms Doke's original suggestion that O is the first ROI produced
    - reference_id: file:ARATH/RBOHD/RBOHD-deep-research-falcon.md
      supporting_text: catalyzes **electron transfer from cytosolic NADPH to
        molecular oxygen (O2)** to generate **superoxide (O2•−)** in the
        **apoplast**, which can subsequently form **H2O2**
references:
- id: file:ARATH/RBOHD/RBOHD-deep-research-falcon.md
  title: Falcon (Edison Scientific) deep research report for RBOHD
  findings: []
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO
    terms
  findings: []
- id: GO_REF:0000108
  title: Automatic assignment of GO terms using logical inference, based on on inter-ontology
    links
  findings: []
- id: GO_REF:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning models
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: GO_REF:0000122
  title: AtSubP analysis
  findings: []
- id: PMID:11756663
  title: Arabidopsis gp91phox homologues AtrbohD and AtrbohF are required for accumulation
    of reactive oxygen intermediates in the plant defense response.
  findings:
  - reference_section_type: ABSTRACT
    supporting_text: AtrbohD and AtrbohF are required for accumulation of reactive
      oxygen intermediates in the plant defense response
  - reference_section_type: DISCUSSION
    supporting_text: an NADPH oxidase subunit is required for ROI production confirms
      Doke's original suggestion that O is the first ROI produced
- id: PMID:15608336
  title: Cytosolic ascorbate peroxidase 1 is a central component of the reactive oxygen
    gene network of Arabidopsis.
  findings: []
- id: PMID:15705948
  title: Different signaling and cell death roles of heterotrimeric G protein alpha
    and beta subunits in the Arabidopsis oxidative stress response to ozone.
  findings: []
- id: PMID:15923322
  title: Heat stress phenotypes of Arabidopsis mutants implicate multiple signaling
    pathways in the acquisition of thermotolerance.
  findings:
  - reference_section_type: ABSTRACT
    supporting_text: Mutations in nicotinamide adenine dinucleotide phosphate oxidase
      homolog genes (atrbohB and D) ... showed weaker defects
- id: PMID:16170317
  title: Pathogen-induced, NADPH oxidase-derived reactive oxygen intermediates suppress
    spread of cell death in Arabidopsis thaliana.
  findings:
  - reference_section_type: ABSTRACT
    supporting_text: the subsequent oxidative burst can suppress cell death in cells
      surrounding sites of NADPH oxidase activation
- id: PMID:19726575
  title: Dual roles of reactive oxygen species and NADPH oxidase RBOHD in an Arabidopsis-Alternaria
    pathosystem.
  findings:
  - reference_section_type: ABSTRACT
    supporting_text: Functional RBOHD causes marked extracellular hydrogen peroxide
      accumulation as well as cell death in distinct, single cells
- id: PMID:21419340
  title: Calmodulin-dependent activation of MAP kinase for ROS homeostasis in Arabidopsis.
  findings:
  - reference_section_type: ABSTRACT
    supporting_text: The MPK8 pathway negatively regulates ROS accumulation through
      controlling expression of the Rboh D gene
- id: PMID:22422940
  title: Osmosensitive changes of carbohydrate metabolism in response to cellulose
    biosynthesis inhibition.
  findings:
  - reference_section_type: ABSTRACT
    supporting_text: osmotic support does not suppress CBI-induced metabolic changes
      in seedlings impaired in ... reactive oxygen species production (respiratory
      burst oxidase homolog DF [rbohDF])
- id: PMID:22430844
  title: Isolation and proteomic characterization of the Arabidopsis Golgi defines
    functional and novel components involved in plant cell wall biosynthesis.
  findings: []
- id: PMID:22923678
  title: Putative glycosyltransferases and other plant Golgi apparatus proteins are
    revealed by LOPIT proteomics.
  findings: []
- id: PMID:24629339
  title: The FLS2-associated kinase BIK1 directly phosphorylates the NADPH oxidase
    RbohD to control plant immunity.
  findings:
  - reference_section_type: ABSTRACT
    supporting_text: the receptor-like cytoplasmic kinase BIK1, a component of the
      FLS2 immune receptor complex, not only positively regulates flg22-triggered
      calcium influx but also directly phosphorylates the NADPH oxidase RbohD at specific
      sites in a calcium-independent manner to enhance ROS generation
- id: PMID:26432875
  title: PBL13 Is a Serine/Threonine Protein Kinase That Negatively Regulates Arabidopsis
    Immune Responses.
  findings:
  - reference_section_type: ABSTRACT
    supporting_text: PBL13 is able to associate with the nicotinamide adenine dinucleotide
      phosphate, reduced oxidase RESPIRATORY BURST OXIDASE HOMOLOG PROTEIN D (RBOHD)
      by split-luciferase complementation assay, and this association is disrupted
      by flagellin treatment
- id: PMID:26704641
  title: 'Arabidopsis HY1-Modulated Stomatal Movement: An Integrative Hub Is Functionally
    Associated with ABI4 in Dehydration-Induced ABA Responsiveness.'
  findings:
  - reference_section_type: ABSTRACT
    supporting_text: the promotion of ABA-triggered up-regulation of RbohD abundance
      and reactive oxygen species (ROS) levels in the hy1 mutant was almost fully
      blocked by the mutation of ABI4
- id: PMID:27251529
  title: Universal stress protein HRU1 mediates ROS homeostasis under anoxia.
  findings:
  - reference_section_type: ABSTRACT
    supporting_text: HRU1 interacts with proteins that induce ROS production, the GTPase
      ROP2 and the NADPH oxidase RbohD, pointing to the existence of a low-oxygen-specific
      mechanism for the modulation of ROS levels
- id: PMID:28696275
  title: A Lectin Receptor-Like Kinase Mediates Pattern-Triggered Salicylic Acid Signaling.
  findings:
  - reference_section_type: ABSTRACT
    supporting_text: LecRK-IX.2 is capable of inducing RbohD phosphorylation, likely
      by recruiting calcium-dependent protein kinases to trigger ROS production in
      Arabidopsis
- id: PMID:28887381
  title: Global Analysis of Membrane-associated Protein Oligomerization Using Protein
    Correlation Profiling.
  findings: []
- id: PMID:31519798
  title: Integrative Analysis from the Epigenome to Translatome Uncovers Patterns
    of Dominant Nuclear Regulation during Transient Stress.
  findings: []
- id: UniProtKB:Q9FIJ0
  title: UniProtKB RBOHD_ARATH (Q9FIJ0) Respiratory burst oxidase homolog protein D.
  findings:
  - reference_section_type: OTHER
    supporting_text: Calcium-dependent NADPH oxidase that generates superoxide.
      Involved in the generation of reactive oxygen species (ROS) during incompatible
      interactions with pathogens, in response to pathogen-associated molecular pattern
      (PAMP)-triggered immunity (PTI) signaling and in UV-B and abscisic acid ROS-dependent
      signaling
core_functions:
- description: Calcium- and phosphorylation-regulated plasma-membrane NADPH oxidase
    that transfers electrons from cytosolic NADPH across the membrane to molecular
    oxygen, generating apoplastic superoxide (the proximal reactive oxygen species,
    which dismutates to hydrogen peroxide). This is the catalytic core function of
    RBOHD.
  molecular_function:
    id: GO:0016175
    label: superoxide-generating NAD(P)H oxidase activity
  directly_involved_in:
  - id: GO:0002679
    label: respiratory burst involved in defense response
  locations:
  - id: GO:0005886
    label: plasma membrane
  supported_by:
  - reference_id: PMID:11756663
    supporting_text: an NADPH oxidase subunit is required for ROI production confirms
      Doke's original suggestion that O is the first ROI produced
  - reference_id: PMID:11756663
    supporting_text: AtrbohD and AtrbohF are required for accumulation of reactive
      oxygen intermediates in the plant defense response
  - reference_id: file:ARATH/RBOHD/RBOHD-deep-research-falcon.md
    supporting_text: catalyzes **electron transfer from cytosolic NADPH to molecular
      oxygen (O2)** to generate **superoxide (O2•−)** in the **apoplast**, which can
      subsequently form **H2O2**
- description: Binds calcium through its two N-terminal EF-hand motifs, conferring
    calcium dependence on oxidase activation; together with phosphorylation by immune
    kinases (e.g. BIK1), calcium binding switches RBOHD into its ROS-producing state
    during pattern-triggered immunity.
  molecular_function:
    id: GO:0005509
    label: calcium ion binding
  directly_involved_in:
  - id: GO:0002679
    label: respiratory burst involved in defense response
  locations:
  - id: GO:0005886
    label: plasma membrane
  supported_by:
  - reference_id: PMID:24629339
    supporting_text: >-
      Here we show that the receptor-like cytoplasmic kinase BIK1, a component of the FLS2
      immune receptor complex, not only positively regulates flg22-triggered calcium influx
      but also directly phosphorylates the NADPH oxidase RbohD at specific sites in a
      calcium-independent manner to enhance ROS generation.
  - reference_id: file:ARATH/RBOHD/RBOHD-deep-research-falcon.md
    supporting_text: RBOHD is activated by direct Ca2+ binding to EF-hands and by phosphorylation
- description: As the principal generator of pathogen-induced extracellular reactive
    oxygen species, RBOHD drives the immune oxidative burst and modulates the spatial
    spread of hypersensitive programmed cell death during plant defense.
  molecular_function:
    id: GO:0016175
    label: superoxide-generating NAD(P)H oxidase activity
  directly_involved_in:
  - id: GO:0006952
    label: defense response
  - id: GO:0043069
    label: negative regulation of programmed cell death
  locations:
  - id: GO:0005886
    label: plasma membrane
  supported_by:
  - reference_id: PMID:11756663
    supporting_text: The AtrbohD gene is required for most of the ROI observed after
      inoculation with avirulent Pst
  - reference_id: PMID:16170317
    supporting_text: the subsequent oxidative burst can suppress cell death in cells
      surrounding sites of NADPH oxidase activation
  - reference_id: file:ARATH/RBOHD/RBOHD-deep-research-falcon.md
    supporting_text: major NADPH oxidase responsible for pathogen-triggered ROS
proposed_new_terms: []
suggested_questions:
- question: Which kinase (BIK1, SIK1, CPKs, LecRK-IX.2) phosphorylation events
    are necessary versus sufficient for RBOHD activation in vivo, and how do
    they integrate with EF-hand calcium binding?
- question: To what extent is RBOHD a hub for the systemic ROS wave, and what
    determines cell-to-cell propagation of its activation across tissues?
- question: How do the recently described negative-regulatory and turnover
    mechanisms (PB1CP-mediated BIK1 displacement and endocytosis,
    PBL13/PIRE-mediated ubiquitination/vacuolar degradation, and CBE1-mediated
    translational repression of RBOHD accumulation) quantitatively shape the
    amplitude and transience of the immune ROS burst?