NaODC_candidate_DCOR

UniProt ID: A0A1J6ITS2
Organism: Nicotiana attenuata
Review Status: DRAFT
Aliases:
DCOR NaODC1 NaODC2
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Gene Description

NaODC_candidate_DCOR is a competing ODC-like paralog in the polyamine branch that feeds nicotine biosynthesis. It is clearly an ornithine decarboxylase family enzyme, but current evidence still favors the ODC accession over DCOR as the primary pathway-specialized copy.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0003824 catalytic activity
IEA
GO_REF:0000002 		MARK AS OVER ANNOTATED
Summary: This parent catalytic term is too generic.
Reason: GO:0004586 already captures the specific chemistry of the DCOR candidate.
GO:0004586 ornithine decarboxylase activity
IEA
GO_REF:0000120 		ACCEPT
Summary: This specific activity annotation is appropriate.
Reason: DCOR is clearly part of the ornithine decarboxylase family and retains the same underlying decarboxylase chemistry.
Supporting Evidence:
file:NICAT/NaODC_candidate_DCOR/NaODC_candidate_DCOR-notes.md
UniProt curates A0A1J6ITS2 as an ornithine decarboxylase-family enzyme that catalyzes the same PLP-dependent ornithine-to-putrescine reaction and is also assigned to nicotine biosynthesis.
GO:0005737 cytoplasm
IEA
GO_REF:0000118 		REMOVE
Summary: Cytoplasm is not the best-supported location for this candidate.
Reason: UniProt supports chloroplast/plastid localization instead of cytoplasm for this accession.
Supporting Evidence:
file:NICAT/NaODC_candidate_DCOR/NaODC_candidate_DCOR-uniprot.txt
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
GO:0006596 polyamine biosynthetic process
IEA
GO_REF:0000002 		ACCEPT
Summary: This process assignment is appropriate.
Reason: Ornithine decarboxylase chemistry directly feeds polyamine biosynthesis via putrescine formation.
GO:0009507 chloroplast
IEA
GO_REF:0000044 		KEEP AS NON CORE
Summary: Chloroplast localization should be retained as non-core context.
Reason: The location is supported, but it is less important than resolving the pathway-specialized ODC paralog.
Supporting Evidence:
file:NICAT/NaODC_candidate_DCOR/NaODC_candidate_DCOR-uniprot.txt
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
GO:0033387 putrescine biosynthetic process from arginine, via ornithine
IEA
GO_REF:0000120 		ACCEPT
Summary: This is the appropriate specific upstream process term.
Reason: DCOR still encodes ornithine-to-putrescine chemistry even if its precise nicotine specialization remains uncertain.
Supporting Evidence:
file:NICAT/NaODC_candidate_DCOR/NaODC_candidate_DCOR-notes.md
UniProt curates A0A1J6ITS2 as an ornithine decarboxylase-family enzyme that catalyzes the same PLP-dependent ornithine-to-putrescine reaction and is also assigned to nicotine biosynthesis.
GO:0042179 nicotine biosynthetic process
IEA
GO_REF:0000041 		KEEP AS NON CORE
Summary: DCOR remains a plausible nicotine-pathway paralog, but the current evidence is not decisive.
Reason: Retain the pathway assignment as a live possibility while acknowledging that ODC is currently the stronger project mapping.
Supporting Evidence:
file:NICAT/NaODC_candidate_DCOR/NaODC_candidate_DCOR-notes.md
DCOR remains a plausible NaODC1/NaODC2 candidate, but current public annotations alone do not show whether it is the specialized nicotine-pathway paralog or a related housekeeping copy.

Core Functions

DCOR is a competing ornithine decarboxylase paralog that retains putrescine biosynthetic chemistry and remains under review for a possible nicotine-pathway role.

Molecular Function:
ornithine decarboxylase activity
Directly Involved In:
putrescine biosynthetic process from arginine, via ornithine
Supporting Evidence:
  • file:NICAT/NaODC_candidate_DCOR/NaODC_candidate_DCOR-notes.md
    DCOR remains a plausible NaODC1/NaODC2 candidate, but current public annotations alone do not show whether it is the specialized nicotine-pathway paralog or a related housekeeping copy.

References

GO_REF:0000002
Gene Ontology annotation through association of InterPro records with GO terms
GO_REF:0000041
Gene Ontology annotation based on UniPathway vocabulary mapping
GO_REF:0000044
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
GO_REF:0000118
TreeGrafter-generated GO annotations
GO_REF:0000120
Combined Automated Annotation using Multiple IEA Methods
file:NICAT/NaODC_candidate_DCOR/NaODC_candidate_DCOR-uniprot.txt
UniProt entry A0A1J6ITS2 for Nicotiana attenuata DCOR
  • DCOR is an ornithine decarboxylase family enzyme
    "DE RecName: Full=ornithine decarboxylase"
  • UniProt places the candidate in nicotine biosynthesis and chloroplast
    "CC -!- PATHWAY: Alkaloid biosynthesis; nicotine biosynthesis."
file:NICAT/NaODC_candidate_DCOR/NaODC_candidate_DCOR-notes.md
NaODC DCOR candidate notes
  • DCOR is a bona fide competing ODC-like paralog
    "UniProt curates A0A1J6ITS2 as an ornithine decarboxylase-family enzyme that catalyzes the same PLP-dependent ornithine-to-putrescine reaction and is also assigned to nicotine biosynthesis."
  • DCOR remains unresolved relative to the stronger ODC candidate
    "DCOR remains a plausible NaODC1/NaODC2 candidate, but current public annotations alone do not show whether it is the specialized nicotine-pathway paralog or a related housekeeping copy."

Suggested Questions for Experts

Q: Is DCOR catalytically equivalent to the stronger ODC candidate, or has it diverged in expression or substrate context?

Q: Does DCOR contribute measurable flux to nicotine biosynthesis or function mainly as a noncore decarboxylase paralog?

Suggested Experiments

Experiment: Compare DCOR and ODC enzymatic activity and expression across root nicotine-inducing conditions.

Hypothesis: DCOR remains catalytically competent but is less tightly coupled to nicotine production than the leading ODC candidate.

Type: comparative biochemistry and expression profiling

Experiment: Measure nicotine-pathway metabolites after selective DCOR perturbation and compare with the primary ODC candidate.

Hypothesis: DCOR has a weaker nicotine phenotype than the leading ODC accession.

Type: comparative genetics plus metabolite profiling

Deep Research

OpenAI

(NaODC_candidate_DCOR-deep-research-openai.md)
**Comprehensive Research Report on NaODC_candidate_DCOR (UniProt Accession: A0A1J6ITS2) in *Nicotiana attenuata*** OpenAI gpt-4.1 10 citations 2026-04-05T13:09:10.605923

Comprehensive Research Report on NaODC_candidate_DCOR (UniProt Accession: A0A1J6ITS2) in Nicotiana attenuata

1. Gene and Protein Identification

  • UniProt Accession: A0A1J6ITS2
  • Protein Description: Ornithine decarboxylase
  • Gene Information: Name=DCOR; ORFNames=A4A49_05809
  • Organism: Nicotiana attenuata (Coyote tobacco)
  • Protein Family: Belongs to the Orn/Lys/Arg decarboxylase class-II family
  • Key Domains:
  • Ala_racemase/Decarboxylase_C (IPR009006)
  • De-COase2_C (IPR022643)
  • De-COase2_CS (IPR022657)
  • De-COase2_N (IPR022644)
  • De-COase2_pyr-phos_BS (IPR022653)

2. Functional Annotation

Ornithine decarboxylase (ODC) is a pivotal enzyme in the biosynthesis of polyamines, catalyzing the decarboxylation of ornithine to produce putrescine. This reaction is the first and rate-limiting step in the polyamine biosynthetic pathway, leading to the formation of spermidine and spermine, compounds essential for cellular functions such as DNA stabilization, cell growth, and differentiation. (en.wikipedia.org)

In Nicotiana attenuata, ODC plays a significant role in the biosynthesis of nicotine, a major alkaloid in this species. Nicotine biosynthesis involves the methylation of putrescine, derived from ornithine via ODC activity, to form N-methylputrescine, a precursor in the nicotine biosynthetic pathway. This underscores the enzyme's critical function in secondary metabolite production, particularly in the formation of defense-related alkaloids. (frontiersin.org)

3. Localization and Expression

ODC expression in Nicotiana attenuata is predominantly localized in the roots, aligning with the root-specific biosynthesis of nicotine. Transcriptome analyses have revealed that genes involved in nicotine biosynthesis, including ODC, exhibit high expression levels in root tissues compared to leaves, flowers, and stems. This root-specific expression pattern is consistent with the localization of nicotine biosynthesis in the roots of N. attenuata. (frontiersin.org)

4. Pathway Involvement

ODC is integral to the polyamine biosynthetic pathway, converting ornithine to putrescine. In Nicotiana attenuata, putrescine serves as a precursor for nicotine biosynthesis. The pathway proceeds as follows:

  1. Ornithine Decarboxylation: ODC catalyzes the conversion of ornithine to putrescine.
  2. Putrescine Methylation: Putrescine is methylated by putrescine N-methyltransferase (PMT) to form N-methylputrescine.
  3. Subsequent Reactions: N-methylputrescine undergoes a series of enzymatic reactions leading to the formation of nicotine.

This pathway highlights the enzyme's role in linking primary metabolism (polyamine biosynthesis) with secondary metabolism (alkaloid biosynthesis), emphasizing its importance in the plant's defense mechanisms. (frontiersin.org)

5. Experimental Evidence and Inference

While direct studies on NaODC_candidate_DCOR in Nicotiana attenuata are limited, functional inferences can be drawn from studies on ODC in related species. In Nicotiana tabacum (common tobacco), down-regulation of ODC via RNA interference resulted in significantly lower concentrations of nicotine and nornicotine, but higher levels of anatabine, indicating ODC's crucial role in nicotine biosynthesis. (pubmed.ncbi.nlm.nih.gov)

Additionally, in Hyoscyamus niger, another member of the Solanaceae family, ODC has been characterized as a rate-limiting enzyme in the biosynthesis of tropane alkaloids, further supporting the enzyme's role in alkaloid biosynthesis in solanaceous plants. (pmc.ncbi.nlm.nih.gov)

Given the conserved nature of the ODC enzyme and its associated pathways across plant species, it is reasonable to infer that NaODC_candidate_DCOR in Nicotiana attenuata functions similarly, contributing to putrescine production and subsequent nicotine biosynthesis.

6. Conclusion

NaODC_candidate_DCOR encodes ornithine decarboxylase in Nicotiana attenuata, an enzyme central to the biosynthesis of polyamines and nicotine. Its root-specific expression aligns with the localization of nicotine biosynthesis, underscoring its role in the plant's defense strategy. While direct experimental data on this specific gene in N. attenuata are scarce, comparative analyses with related species provide substantial evidence for its functional annotation.

References

📚 Additional Documentation

Notes

(NaODC_candidate_DCOR-notes.md)

NaODC_candidate_DCOR Notes

  • UniProt curates A0A1J6ITS2 as an ornithine decarboxylase-family enzyme that catalyzes the same PLP-dependent ornithine-to-putrescine reaction and is also assigned to nicotine biosynthesis. [file:NICAT/NaODC_candidate_DCOR/NaODC_candidate_DCOR-uniprot.txt "DE RecName: Full=ornithine decarboxylase"; "CC -!- CATALYTIC ACTIVITY: Reaction=L-ornithine + H(+) = putrescine + CO2"; "CC -!- PATHWAY: Alkaloid biosynthesis; nicotine biosynthesis."; "CC -!- PATHWAY: Amine and polyamine biosynthesis; putrescine biosynthesis via L-ornithine pathway; putrescine from L-ornithine: step 1/1."]
  • UniProt places this candidate in plastid/chloroplast and in the same class-II ornithine/lysine/arginine decarboxylase family, so DCOR is not an unrelated decarboxylase but a bona fide competing ODC-like paralog. [file:NICAT/NaODC_candidate_DCOR/NaODC_candidate_DCOR-uniprot.txt "CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast"; "CC -!- SIMILARITY: Belongs to the Orn/Lys/Arg decarboxylase class-II family."; "DR PANTHER; PTHR11482:SF6; ORNITHINE DECARBOXYLASE 1-RELATED; 1."]
  • The N. attenuata genome paper makes duplicated polyamine-pathway ancestry a central feature of nicotine-pathway evolution, which is exactly why the ODC versus DCOR split has to be reviewed explicitly. PMID:28536194
  • The full glucosylation preprint keeps the upstream ODC-PMT-MPO module inside the minimal reconstituted pathway, so even a competing DCOR-like paralog remains relevant until the ODC-family split is resolved directly. [file:projects/NICOTINE_BIOSYNTHESIS/biorxiv-nicotine-glucosylation-notes.md "In N. benthamiana leaves, the in planta reconstruction uses ODC, PMT, and MPO to generate N-methylpyrrolinium, then depends on the glucosylation-late-pathway module to make labelled nicotine"; "ODC, PMT, and MPO remain part of the minimal upstream module needed to feed the completed pathway."]
  • DCOR remains a plausible NaODC1/NaODC2 candidate, but current public annotations alone do not show whether it is the specialized nicotine-pathway paralog or a related housekeeping copy. [file:NICAT/NaODC_candidate_DCOR/NaODC_candidate_DCOR-uniprot.txt "GN Name=DCOR"; "CC -!- PATHWAY: Alkaloid biosynthesis; nicotine biosynthesis."]

📄 View Raw YAML

 
id: A0A1J6ITS2
gene_symbol: NaODC_candidate_DCOR
product_type: PROTEIN
status: DRAFT
aliases:
- DCOR
- NaODC1
- NaODC2
taxon:
  id: NCBITaxon:49451
  label: Nicotiana attenuata
description: >-
  NaODC_candidate_DCOR is a competing ODC-like paralog in the polyamine branch
  that feeds nicotine biosynthesis. It is clearly an ornithine decarboxylase
  family enzyme, but current evidence still favors the ODC accession over DCOR as
  the primary pathway-specialized copy.
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms
  findings: []
- id: GO_REF:0000041
  title: Gene Ontology annotation based on UniPathway vocabulary mapping
  findings: []
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
  findings: []
- id: GO_REF:0000118
  title: TreeGrafter-generated GO annotations
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: file:NICAT/NaODC_candidate_DCOR/NaODC_candidate_DCOR-uniprot.txt
  title: UniProt entry A0A1J6ITS2 for Nicotiana attenuata DCOR
  findings:
  - statement: DCOR is an ornithine decarboxylase family enzyme
    supporting_text: 'DE   RecName: Full=ornithine decarboxylase'
    reference_section_type: DATABASE_ENTRY
  - statement: UniProt places the candidate in nicotine biosynthesis and chloroplast
    supporting_text: 'CC   -!- PATHWAY: Alkaloid biosynthesis; nicotine biosynthesis.'
    reference_section_type: DATABASE_ENTRY
- id: file:NICAT/NaODC_candidate_DCOR/NaODC_candidate_DCOR-notes.md
  title: NaODC DCOR candidate notes
  findings:
  - statement: DCOR is a bona fide competing ODC-like paralog
    supporting_text: UniProt curates A0A1J6ITS2 as an ornithine decarboxylase-family enzyme that catalyzes the same PLP-dependent ornithine-to-putrescine reaction and is also assigned to nicotine biosynthesis.
    reference_section_type: LITERATURE_REVIEW
  - statement: DCOR remains unresolved relative to the stronger ODC candidate
    supporting_text: DCOR remains a plausible NaODC1/NaODC2 candidate, but current public annotations alone do not show whether it is the specialized nicotine-pathway paralog or a related housekeeping copy.
    reference_section_type: LITERATURE_REVIEW
existing_annotations:
- term:
    id: GO:0003824
    label: catalytic activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: This parent catalytic term is too generic.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      GO:0004586 already captures the specific chemistry of the DCOR candidate.
- term:
    id: GO:0004586
    label: ornithine decarboxylase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: This specific activity annotation is appropriate.
    action: ACCEPT
    reason: >-
      DCOR is clearly part of the ornithine decarboxylase family and retains the
      same underlying decarboxylase chemistry.
    supported_by:
    - reference_id: file:NICAT/NaODC_candidate_DCOR/NaODC_candidate_DCOR-notes.md
      supporting_text: UniProt curates A0A1J6ITS2 as an ornithine decarboxylase-family enzyme that catalyzes the same PLP-dependent ornithine-to-putrescine reaction and is also assigned to nicotine biosynthesis.
      reference_section_type: LITERATURE_REVIEW
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000118
  review:
    summary: Cytoplasm is not the best-supported location for this candidate.
    action: REMOVE
    reason: >-
      UniProt supports chloroplast/plastid localization instead of cytoplasm for
      this accession.
    supported_by:
    - reference_id: file:NICAT/NaODC_candidate_DCOR/NaODC_candidate_DCOR-uniprot.txt
      supporting_text: 'CC   -!- SUBCELLULAR LOCATION: Plastid, chloroplast'
      reference_section_type: DATABASE_ENTRY
- term:
    id: GO:0006596
    label: polyamine biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: This process assignment is appropriate.
    action: ACCEPT
    reason: >-
      Ornithine decarboxylase chemistry directly feeds polyamine biosynthesis via
      putrescine formation.
- term:
    id: GO:0009507
    label: chloroplast
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: Chloroplast localization should be retained as non-core context.
    action: KEEP_AS_NON_CORE
    reason: >-
      The location is supported, but it is less important than resolving the
      pathway-specialized ODC paralog.
    supported_by:
    - reference_id: file:NICAT/NaODC_candidate_DCOR/NaODC_candidate_DCOR-uniprot.txt
      supporting_text: 'CC   -!- SUBCELLULAR LOCATION: Plastid, chloroplast'
      reference_section_type: DATABASE_ENTRY
- term:
    id: GO:0033387
    label: putrescine biosynthetic process from arginine, via ornithine
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: This is the appropriate specific upstream process term.
    action: ACCEPT
    reason: >-
      DCOR still encodes ornithine-to-putrescine chemistry even if its precise
      nicotine specialization remains uncertain.
    supported_by:
    - reference_id: file:NICAT/NaODC_candidate_DCOR/NaODC_candidate_DCOR-notes.md
      supporting_text: UniProt curates A0A1J6ITS2 as an ornithine decarboxylase-family enzyme that catalyzes the same PLP-dependent ornithine-to-putrescine reaction and is also assigned to nicotine biosynthesis.
      reference_section_type: LITERATURE_REVIEW
- term:
    id: GO:0042179
    label: nicotine biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000041
  review:
    summary: DCOR remains a plausible nicotine-pathway paralog, but the current evidence is not decisive.
    action: KEEP_AS_NON_CORE
    reason: >-
      Retain the pathway assignment as a live possibility while acknowledging that
      ODC is currently the stronger project mapping.
    supported_by:
    - reference_id: file:NICAT/NaODC_candidate_DCOR/NaODC_candidate_DCOR-notes.md
      supporting_text: DCOR remains a plausible NaODC1/NaODC2 candidate, but current public annotations alone do not show whether it is the specialized nicotine-pathway paralog or a related housekeeping copy.
      reference_section_type: LITERATURE_REVIEW
core_functions:
- molecular_function:
    id: GO:0004586
    label: ornithine decarboxylase activity
  directly_involved_in:
  - id: GO:0033387
    label: putrescine biosynthetic process from arginine, via ornithine
  description: >-
    DCOR is a competing ornithine decarboxylase paralog that retains putrescine
    biosynthetic chemistry and remains under review for a possible nicotine-pathway
    role.
  supported_by:
  - reference_id: file:NICAT/NaODC_candidate_DCOR/NaODC_candidate_DCOR-notes.md
    supporting_text: DCOR remains a plausible NaODC1/NaODC2 candidate, but current public annotations alone do not show whether it is the specialized nicotine-pathway paralog or a related housekeeping copy.
    reference_section_type: LITERATURE_REVIEW
proposed_new_terms: []
suggested_questions:
- question: Is DCOR catalytically equivalent to the stronger ODC candidate, or has it diverged in expression or substrate context?
- question: Does DCOR contribute measurable flux to nicotine biosynthesis or function mainly as a noncore decarboxylase paralog?
suggested_experiments:
- description: Compare DCOR and ODC enzymatic activity and expression across root nicotine-inducing conditions.
  experiment_type: comparative biochemistry and expression profiling
  hypothesis: DCOR remains catalytically competent but is less tightly coupled to nicotine production than the leading ODC candidate.
- description: Measure nicotine-pathway metabolites after selective DCOR perturbation and compare with the primary ODC candidate.
  experiment_type: comparative genetics plus metabolite profiling
  hypothesis: DCOR has a weaker nicotine phenotype than the leading ODC accession.