NaODC_candidate_ODC is an ornithine decarboxylase candidate for the polyamine branch that feeds nicotine biosynthesis in Nicotiana attenuata. It catalyzes putrescine formation from ornithine and is a strong candidate for the ODC step in the upstream N-methylpyrrolinium module.
| 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 informative enzymatic chemistry for this accession.
|
|
GO:0004586
ornithine decarboxylase activity
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: This is the core molecular-function annotation for the candidate.
Reason: UniProt explicitly identifies ornithine-to-putrescine decarboxylation for this accession.
Supporting Evidence:
file:NICAT/NaODC_candidate_ODC/NaODC_candidate_ODC-notes.md
UniProt curates A0A314KUM9 as ornithine decarboxylase, catalyzing the PLP-dependent conversion of L-ornithine to putrescine and assigning the protein to both putrescine and nicotine biosynthesis.
|
|
GO:0005737
cytoplasm
|
IEA
GO_REF:0000118 |
REMOVE |
Summary: Cytoplasmic localization is not the best-supported location for this candidate.
Reason: UniProt supports chloroplast/plastid localization instead, so the TreeGrafter cytoplasm inference is not the preferred assignment.
Supporting Evidence:
file:NICAT/NaODC_candidate_ODC/NaODC_candidate_ODC-uniprot.txt
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
|
|
GO:0006596
polyamine biosynthetic process
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: This is an appropriate process annotation.
Reason: Ornithine decarboxylase provides putrescine to the polyamine pathway.
|
|
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 in UniProt, but the more important issue here is pathway membership and paralog ranking.
Supporting Evidence:
file:NICAT/NaODC_candidate_ODC/NaODC_candidate_ODC-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 specific upstream biological process driven by ODC.
Reason: ODC catalyzes the step that converts ornithine to putrescine in the route feeding nicotine biosynthesis.
Supporting Evidence:
file:NICAT/NaODC_candidate_ODC/NaODC_candidate_ODC-notes.md
UniProt curates A0A314KUM9 as ornithine decarboxylase, catalyzing the PLP-dependent conversion of L-ornithine to putrescine and assigning the protein to both putrescine and nicotine biosynthesis.
|
|
GO:0042179
nicotine biosynthetic process
|
IEA
GO_REF:0000041 |
ACCEPT |
Summary: This is an appropriate pathway annotation for the leading ODC candidate.
Reason: The ODC step is part of the upstream module that feeds the N-methylpyrrolinium branch, and this accession is the stronger current ODC mapping.
Supporting Evidence:
file:NICAT/NaODC_candidate_ODC/NaODC_candidate_ODC-notes.md
This accession is therefore a strong NaODC1/NaODC2 candidate, but resolving it against the DCOR paralog still requires evidence beyond current automated pathway annotation.
|
Q: Is this ODC accession the dominant nicotine-feeding paralog in roots, or does the DCOR-related copy make a substantial parallel contribution?
Q: Does chloroplast localization materially constrain where putrescine enters the nicotine pathway in Nicotiana attenuata?
Experiment: Compare ODC and DCOR activity, expression, and root nicotine phenotypes after selective perturbation of each paralog.
Hypothesis: The ODC accession is the major nicotine-feeding ornithine decarboxylase paralog.
Type: comparative genetics and biochemistry
Experiment: Quantify putrescine, N-methylputrescine, and nicotine levels after ODC disruption under topping or herbivory induction.
Hypothesis: Loss of the leading ODC candidate will reduce flux into the pyrrolidine branch.
Type: metabolite profiling after genetic perturbation
Ornithine decarboxylase (ODC) is a pivotal enzyme in the biosynthesis of polyamines, catalyzing the decarboxylation of L-ornithine to produce putrescine. This reaction represents the initial and rate-limiting step in the synthesis of polyamines such as spermidine and spermine, which are essential for various cellular processes, including DNA stabilization, cell growth, and differentiation.
Function and Enzymatic Activity
In Nicotiana attenuata (coyote tobacco), ODC plays a crucial role in the production of putrescine, a precursor not only for polyamines but also for alkaloids like nicotine. The enzyme's activity is dependent on the cofactor pyridoxal-5'-phosphate (PLP), which facilitates the decarboxylation process. The reaction can be summarized as follows:
[ \text{L-ornithine} \xrightarrow{\text{ODC}} \text{Putrescine} + \text{CO}_2 ]
This enzymatic function is critical for the plant's secondary metabolism, particularly in the synthesis of defensive compounds such as nicotine.
Biological Processes and Localization
ODC is predominantly expressed in the roots of Nicotiana attenuata, 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. This root-specific expression pattern underscores the enzyme's role in the localized production of alkaloids, which are then transported to aerial parts of the plant to deter herbivory. (frontiersin.org)
Pathways and Metabolic Integration
ODC's activity integrates into the broader polyamine biosynthetic pathway, influencing both primary and secondary metabolism. The putrescine produced by ODC serves as a substrate for the synthesis of spermidine and spermine, polyamines that are vital for cellular functions. Additionally, putrescine is a precursor for nicotine biosynthesis in Nicotiana species. Studies in Nicotiana tabacum have demonstrated that down-regulation of ODC leads to decreased levels of nicotine and nornicotine, accompanied by increased levels of anatabine. This alteration suggests that ODC activity directly affects the flux through the nicotine biosynthetic pathway. (pubmed.ncbi.nlm.nih.gov)
Structural Insights and Evolutionary Considerations
ODC belongs to the Orn/Lys/Arg decarboxylase class-II family, characterized by specific structural domains:
Ala_racemase/Decarboxylase_C (IPR009006): This domain is involved in the catalytic activity of the enzyme.
De-COase2_N (IPR022644): This N-terminal domain contributes to the enzyme's structural stability.
De-COase2_pyr-phos_BS (IPR022653): This domain is associated with the binding of the pyridoxal-5'-phosphate cofactor.
Orn/DAP/Arg_de-COase (IPR000183): This domain is common among decarboxylases acting on ornithine, diaminopimelate, and arginine.
Orn_de-COase (IPR002433): This domain is specific to ornithine decarboxylases.
These domains collectively facilitate the enzyme's function and stability. Comparative studies have shown that plant ODCs, such as those from Nicotiana glutinosa, share significant sequence identity with ODCs from other plant species, indicating a conserved evolutionary role in polyamine and alkaloid biosynthesis. (pubmed.ncbi.nlm.nih.gov)
Conclusion
In Nicotiana attenuata, ornithine decarboxylase is integral to the biosynthesis of polyamines and alkaloids, particularly nicotine. Its root-specific expression aligns with the localized production of these compounds, which are essential for the plant's defense mechanisms. The enzyme's activity, structural domains, and evolutionary conservation underscore its critical role in plant metabolism and adaptation.
The YAML description field was revised to keep it as a standalone biological summary. Project-specific curation framing moved here instead.
id: A0A314KUM9
gene_symbol: NaODC_candidate_ODC
product_type: PROTEIN
status: DRAFT
aliases:
- ODC
- NaODC1
- NaODC2
taxon:
id: NCBITaxon:49451
label: Nicotiana attenuata
description: >-
NaODC_candidate_ODC is an ornithine decarboxylase candidate for the polyamine branch that feeds
nicotine biosynthesis in Nicotiana attenuata. It catalyzes putrescine formation from ornithine and
is a strong candidate for the ODC step in the upstream N-methylpyrrolinium module.
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_ODC/NaODC_candidate_ODC-uniprot.txt
title: UniProt entry A0A314KUM9 for Nicotiana attenuata ODC
findings:
- statement: ODC catalyzes ornithine decarboxylation to putrescine
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_ODC/NaODC_candidate_ODC-notes.md
title: NaODC ODC candidate notes
findings:
- statement: ODC is a strong nicotine-module candidate for putrescine supply
supporting_text: UniProt curates A0A314KUM9 as ornithine decarboxylase, catalyzing the PLP-dependent conversion of L-ornithine to putrescine and assigning the protein to both putrescine and nicotine biosynthesis.
reference_section_type: LITERATURE_REVIEW
- statement: ODC remains stronger than DCOR as the current primary ODC mapping
supporting_text: This accession is therefore a strong NaODC1/NaODC2 candidate, but resolving it against the DCOR paralog still requires evidence beyond current automated pathway annotation.
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 informative enzymatic chemistry for this
accession.
- term:
id: GO:0004586
label: ornithine decarboxylase activity
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: This is the core molecular-function annotation for the candidate.
action: ACCEPT
reason: >-
UniProt explicitly identifies ornithine-to-putrescine decarboxylation for
this accession.
supported_by:
- reference_id: file:NICAT/NaODC_candidate_ODC/NaODC_candidate_ODC-notes.md
supporting_text: UniProt curates A0A314KUM9 as ornithine decarboxylase, catalyzing the PLP-dependent conversion of L-ornithine to putrescine and assigning the protein to both putrescine and nicotine biosynthesis.
reference_section_type: LITERATURE_REVIEW
- term:
id: GO:0005737
label: cytoplasm
evidence_type: IEA
original_reference_id: GO_REF:0000118
review:
summary: Cytoplasmic localization is not the best-supported location for this candidate.
action: REMOVE
reason: >-
UniProt supports chloroplast/plastid localization instead, so the TreeGrafter
cytoplasm inference is not the preferred assignment.
supported_by:
- reference_id: file:NICAT/NaODC_candidate_ODC/NaODC_candidate_ODC-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 is an appropriate process annotation.
action: ACCEPT
reason: >-
Ornithine decarboxylase provides putrescine to the polyamine pathway.
- 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 in UniProt, but the more important issue here is
pathway membership and paralog ranking.
supported_by:
- reference_id: file:NICAT/NaODC_candidate_ODC/NaODC_candidate_ODC-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 specific upstream biological process driven by ODC.
action: ACCEPT
reason: >-
ODC catalyzes the step that converts ornithine to putrescine in the route
feeding nicotine biosynthesis.
supported_by:
- reference_id: file:NICAT/NaODC_candidate_ODC/NaODC_candidate_ODC-notes.md
supporting_text: UniProt curates A0A314KUM9 as ornithine decarboxylase, catalyzing the PLP-dependent conversion of L-ornithine to putrescine and assigning the protein to both putrescine and 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: This is an appropriate pathway annotation for the leading ODC candidate.
action: ACCEPT
reason: >-
The ODC step is part of the upstream module that feeds the N-methylpyrrolinium
branch, and this accession is the stronger current ODC mapping.
supported_by:
- reference_id: file:NICAT/NaODC_candidate_ODC/NaODC_candidate_ODC-notes.md
supporting_text: This accession is therefore a strong NaODC1/NaODC2 candidate, but resolving it against the DCOR paralog still requires evidence beyond current automated pathway annotation.
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
- id: GO:0042179
label: nicotine biosynthetic process
description: >-
ODC catalyzes the conversion of ornithine to putrescine, supplying the
upstream polyamine-derived branch that feeds nicotine biosynthesis.
supported_by:
- reference_id: file:NICAT/NaODC_candidate_ODC/NaODC_candidate_ODC-notes.md
supporting_text: UniProt curates A0A314KUM9 as ornithine decarboxylase, catalyzing the PLP-dependent conversion of L-ornithine to putrescine and assigning the protein to both putrescine and nicotine biosynthesis.
reference_section_type: LITERATURE_REVIEW
proposed_new_terms: []
suggested_questions:
- question: Is this ODC accession the dominant nicotine-feeding paralog in roots, or does the DCOR-related copy make a substantial parallel contribution?
- question: Does chloroplast localization materially constrain where putrescine enters the nicotine pathway in Nicotiana attenuata?
suggested_experiments:
- description: Compare ODC and DCOR activity, expression, and root nicotine phenotypes after selective perturbation of each paralog.
experiment_type: comparative genetics and biochemistry
hypothesis: The ODC accession is the major nicotine-feeding ornithine decarboxylase paralog.
- description: Quantify putrescine, N-methylputrescine, and nicotine levels after ODC disruption under topping or herbivory induction.
experiment_type: metabolite profiling after genetic perturbation
hypothesis: Loss of the leading ODC candidate will reduce flux into the pyrrolidine branch.