Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0004514 nicotinate-nucleotide diphosphorylase (carboxylating) activity	IEA GO_REF:0000120	ACCEPT	Summary: This is the core catalytic annotation for QPT_0. Reason: UniProt and the protein family assignment consistently identify the quinolinate phosphoribosyltransferase reaction. Supporting Evidence: file:NICAT/NaQPT2_candidate_QPT_0/NaQPT2_candidate_QPT_0-notes.md UniProt curates A0A1J6KEF3 as nicotinate-nucleotide diphosphorylase (carboxylating), the quinolinate phosphoribosyltransferase/NadC reaction that connects quinolinate metabolism to NAD and nicotine pathway annotations.
GO:0005737 cytoplasm	IEA GO_REF:0000118	KEEP AS NON CORE	Summary: Cytoplasmic localization is plausible but not central to this review. Reason: Retain the location as reasonable contextual information while focusing on catalytic chemistry and paralog resolution.
GO:0009435 NAD+ biosynthetic process	IEA GO_REF:0000120	ACCEPT	Summary: QPT_0 belongs in de novo NAD biosynthesis. Reason: The quinolinate phosphoribosyltransferase step is a standard part of the NAD pathway that underlies the nicotine pyridine branch. Supporting Evidence: file:NICAT/NaQPT2_candidate_QPT_0/NaQPT2_candidate_QPT_0-notes.md UniProt curates A0A1J6KEF3 as nicotinate-nucleotide diphosphorylase (carboxylating), the quinolinate phosphoribosyltransferase/NadC reaction that connects quinolinate metabolism to NAD and nicotine pathway annotations.
GO:0009611 response to wounding	IEA GO_REF:0000117	KEEP AS NON CORE	Summary: This regulatory-context annotation is plausible but not strongly resolved for QPT_0 specifically. Reason: Nicotine-pathway genes are often inducible by damage cues, but the key curation issue here is enzymatic and paralog-specific rather than response biology.
GO:0016763 pentosyltransferase activity	IEA GO_REF:0000002	MODIFY	Summary: This broader transferase term is directionally correct but should be replaced by the specific QPT activity term. Reason: GO:0004514 already captures the exact catalytic chemistry for this protein. Proposed replacements: nicotinate-nucleotide diphosphorylase (carboxylating) activity
GO:0034213 quinolinate catabolic process	IEA GO_REF:0000118	ACCEPT	Summary: This process annotation fits the known QPT reaction. Reason: QPT converts quinolinate into nicotinate mononucleotide and therefore participates directly in quinolinate consumption.
GO:0042179 nicotine biosynthetic process	IEA GO_REF:0000041	KEEP AS NON CORE	Summary: QPT_0 is a plausible nicotine-pathway candidate, but exact paralog assignment remains open. Reason: Family-level and UniProt evidence keep QPT_0 in scope for the nicotine pyridine branch, yet the current data do not conclusively rank it above QPT_1 as the specialized root copy. Supporting Evidence: file:NICAT/NaQPT2_candidate_QPT_0/NaQPT2_candidate_QPT_0-notes.md QPT_0 is therefore a plausible NaQPT2 candidate, but the current public record does not by itself establish whether QPT_0 or QPT_1 is the root nicotine-pathway-specialized paralog.

Core Functions

QPT_0 catalyzes the quinolinate phosphoribosyltransferase step of de novo NAD biosynthesis and is a plausible duplicated pyridine-branch contributor to nicotine biosynthesis.

Molecular Function:

nicotinate-nucleotide diphosphorylase (carboxylating) activity

Directly Involved In:

NAD+ biosynthetic process quinolinate catabolic process

Supporting Evidence:

file:NICAT/NaQPT2_candidate_QPT_0/NaQPT2_candidate_QPT_0-notes.md
UniProt curates A0A1J6KEF3 as nicotinate-nucleotide diphosphorylase (carboxylating), the quinolinate phosphoribosyltransferase/NadC reaction that connects quinolinate metabolism to NAD and nicotine pathway annotations.

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:0000117

Electronic Gene Ontology annotations created by ARBA machine learning models

GO_REF:0000118

TreeGrafter-generated GO annotations

GO_REF:0000120

Combined Automated Annotation using Multiple IEA Methods

file:NICAT/NaQPT2_candidate_QPT_0/NaQPT2_candidate_QPT_0-uniprot.txt

UniProt entry A0A1J6KEF3 for Nicotiana attenuata QPT_0

QPT_0 is a quinolinate phosphoribosyltransferase family enzyme

"DE RecName: Full=nicotinate-nucleotide diphosphorylase (carboxylating)"
UniProt places QPT_0 in both NAD and nicotine pathway annotations

"CC -!- PATHWAY: Alkaloid biosynthesis; nicotine biosynthesis."

file:NICAT/NaQPT2_candidate_QPT_0/NaQPT2_candidate_QPT_0-notes.md

NaQPT2 QPT_0 candidate notes

QPT_0 is a strong biochemical candidate for the duplicated pyridine branch

"UniProt curates A0A1J6KEF3 as nicotinate-nucleotide diphosphorylase (carboxylating), the quinolinate phosphoribosyltransferase/NadC reaction that connects quinolinate metabolism to NAD and nicotine pathway annotations."
QPT_0 remains unresolved relative to QPT_1 for pathway specialization

"QPT_0 is therefore a plausible NaQPT2 candidate, but the current public record does not by itself establish whether QPT_0 or QPT_1 is the root nicotine-pathway-specialized paralog."

Suggested Experiments

Experiment: Compare QPT_0 and QPT_1 enzymatic activity and transcript abundance across nicotine-inducing conditions in roots.

Hypothesis: One QPT paralog is specialized for the nicotine-associated pyridine branch.

Type: comparative biochemistry and expression profiling

Experiment: Perturb QPT_0 and QPT_1 individually and quantify quinolinate, nicotinate ribonucleotide, and nicotine levels in roots.

Hypothesis: The pathway-specialized QPT paralog will have a stronger effect on nicotine precursor supply.

Type: genetics plus metabolite profiling

Deep Research

OpenAI

(NaQPT2_candidate_QPT_0-deep-research-openai.md)

NaQPT2_candidate_QPT_0-deep-research-openai OpenAI gpt-4.1 2 citations 2026-04-05T13:08:19.949467

The nicotinate-nucleotide diphosphorylase (carboxylating) encoded by the NaQPT2_candidate_QPT_0 gene in Nicotiana attenuata is a crucial enzyme in the de novo NAD⁺ biosynthesis pathway. Its activity ensures the production of NAD⁺, supporting essential metabolic processes and stress responses in the plant. While specific studies in Nicotiana attenuata are limited, the enzyme's function can be inferred from its conserved role and structural domains shared with homologous proteins in other species.

📚 Additional Documentation

Notes

(NaQPT2_candidate_QPT_0-notes.md)

NaQPT2_candidate_QPT_0 Notes

UniProt curates A0A1J6KEF3 as nicotinate-nucleotide diphosphorylase (carboxylating), the quinolinate phosphoribosyltransferase/NadC reaction that connects quinolinate metabolism to NAD and nicotine pathway annotations. [file:NICAT/NaQPT2_candidate_QPT_0/NaQPT2_candidate_QPT_0-uniprot.txt "DE RecName: Full=nicotinate-nucleotide diphosphorylase (carboxylating)"; "CC -!- CATALYTIC ACTIVITY: Reaction=nicotinate beta-D-ribonucleotide + CO2 + diphosphate = quinolinate + 5-phospho-alpha-D-ribose 1-diphosphate + 2 H(+)"; "CC -!- PATHWAY: Alkaloid biosynthesis; nicotine biosynthesis."; "CC -!- PATHWAY: Cofactor biosynthesis; NAD(+) biosynthesis; nicotinate D-ribonucleotide from quinolinate: step 1/1."]
UniProt places this candidate in the NadC/ModD family and assigns both NAD+ biosynthetic process and nicotine biosynthetic process, which makes QPT_0 a strong biochemical candidate for the duplicated pyridine branch. [file:NICAT/NaQPT2_candidate_QPT_0/NaQPT2_candidate_QPT_0-uniprot.txt "CC -!- SIMILARITY: Belongs to the NadC/ModD family."; "DR GO; GO:0009435; P:NAD+ biosynthetic process; IEA:UniProtKB-UniPathway."; "DR GO; GO:0042179; P:nicotine biosynthetic process; IEA:UniProtKB-UniPathway."]
The N. attenuata genome paper argues that nicotine biosynthesis emerged from duplicated NAD-pathway genes, which is the core rationale for reviewing multiple QPT paralogs instead of accepting both automatically. PMID:28536194
The full glucosylation preprint keeps QPT2 tied to the modern nicotine module by listing it among the stronger tobacco genes correlated with UGT1, but that remains coexpression evidence rather than direct enzymology. [file:projects/NICOTINE_BIOSYNTHESIS/biorxiv-nicotine-glucosylation-notes.md "genes most correlated with UGT1 include BBLa, QPT2, beta-GD1, A622, PMT1, PMT2, PMT3, and MATE1"; "QPT2 and AO2 are supported at the level of coordinated pathway expression and pathway framing, but this paper does not directly assay their enzymatic roles."]
QPT_0 is therefore a plausible NaQPT2 candidate, but the current public record does not by itself establish whether QPT_0 or QPT_1 is the root nicotine-pathway-specialized paralog. [file:NICAT/NaQPT2_candidate_QPT_0/NaQPT2_candidate_QPT_0-uniprot.txt "GN Name=QPT_0"; "CC -!- PATHWAY: Alkaloid biosynthesis; nicotine biosynthesis."]

📄 View Raw YAML

id: A0A1J6KEF3
gene_symbol: NaQPT2_candidate_QPT_0
product_type: PROTEIN
status: DRAFT
aliases:
- QPT_0
- NaQPT2
taxon:
  id: NCBITaxon:49451
  label: Nicotiana attenuata
description: >-
  NaQPT2_candidate_QPT_0 is one of the two current NICAT quinolinate
  phosphoribosyltransferase candidates for the duplicated pyridine branch of
  nicotine biosynthesis. It clearly encodes a nicotinate-nucleotide
  diphosphorylase in NAD precursor metabolism, but the exact pathway-specialized
  paralog remains unresolved.
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:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning models
  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/NaQPT2_candidate_QPT_0/NaQPT2_candidate_QPT_0-uniprot.txt
  title: UniProt entry A0A1J6KEF3 for Nicotiana attenuata QPT_0
  findings:
  - statement: QPT_0 is a quinolinate phosphoribosyltransferase family enzyme
    supporting_text: 'DE   RecName: Full=nicotinate-nucleotide diphosphorylase (carboxylating)'
    reference_section_type: DATABASE_ENTRY
  - statement: UniProt places QPT_0 in both NAD and nicotine pathway annotations
    supporting_text: 'CC   -!- PATHWAY: Alkaloid biosynthesis; nicotine biosynthesis.'
    reference_section_type: DATABASE_ENTRY
- id: file:NICAT/NaQPT2_candidate_QPT_0/NaQPT2_candidate_QPT_0-notes.md
  title: NaQPT2 QPT_0 candidate notes
  findings:
  - statement: QPT_0 is a strong biochemical candidate for the duplicated pyridine branch
    supporting_text: UniProt curates A0A1J6KEF3 as nicotinate-nucleotide diphosphorylase (carboxylating), the quinolinate phosphoribosyltransferase/NadC reaction that connects quinolinate metabolism to NAD and nicotine pathway annotations.
    reference_section_type: LITERATURE_REVIEW
  - statement: QPT_0 remains unresolved relative to QPT_1 for pathway specialization
    supporting_text: QPT_0 is therefore a plausible NaQPT2 candidate, but the current public record does not by itself establish whether QPT_0 or QPT_1 is the root nicotine-pathway-specialized paralog.
    reference_section_type: LITERATURE_REVIEW
existing_annotations:
- term:
    id: GO:0004514
    label: nicotinate-nucleotide diphosphorylase (carboxylating) activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: This is the core catalytic annotation for QPT_0.
    action: ACCEPT
    reason: >-
      UniProt and the protein family assignment consistently identify the
      quinolinate phosphoribosyltransferase reaction.
    supported_by:
    - reference_id: file:NICAT/NaQPT2_candidate_QPT_0/NaQPT2_candidate_QPT_0-notes.md
      supporting_text: UniProt curates A0A1J6KEF3 as nicotinate-nucleotide diphosphorylase (carboxylating), the quinolinate phosphoribosyltransferase/NadC reaction that connects quinolinate metabolism to NAD and nicotine pathway annotations.
      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 plausible but not central to this review.
    action: KEEP_AS_NON_CORE
    reason: >-
      Retain the location as reasonable contextual information while focusing on
      catalytic chemistry and paralog resolution.
- term:
    id: GO:0009435
    label: NAD+ biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: QPT_0 belongs in de novo NAD biosynthesis.
    action: ACCEPT
    reason: >-
      The quinolinate phosphoribosyltransferase step is a standard part of the NAD
      pathway that underlies the nicotine pyridine branch.
    supported_by:
    - reference_id: file:NICAT/NaQPT2_candidate_QPT_0/NaQPT2_candidate_QPT_0-notes.md
      supporting_text: UniProt curates A0A1J6KEF3 as nicotinate-nucleotide diphosphorylase (carboxylating), the quinolinate phosphoribosyltransferase/NadC reaction that connects quinolinate metabolism to NAD and nicotine pathway annotations.
      reference_section_type: LITERATURE_REVIEW
- term:
    id: GO:0009611
    label: response to wounding
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: This regulatory-context annotation is plausible but not strongly resolved for QPT_0 specifically.
    action: KEEP_AS_NON_CORE
    reason: >-
      Nicotine-pathway genes are often inducible by damage cues, but the key
      curation issue here is enzymatic and paralog-specific rather than response
      biology.
- term:
    id: GO:0016763
    label: pentosyltransferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: This broader transferase term is directionally correct but should be replaced by the specific QPT activity term.
    action: MODIFY
    reason: >-
      GO:0004514 already captures the exact catalytic chemistry for this protein.
    proposed_replacement_terms:
    - id: GO:0004514
      label: nicotinate-nucleotide diphosphorylase (carboxylating) activity
- term:
    id: GO:0034213
    label: quinolinate catabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000118
  review:
    summary: This process annotation fits the known QPT reaction.
    action: ACCEPT
    reason: >-
      QPT converts quinolinate into nicotinate mononucleotide and therefore
      participates directly in quinolinate consumption.
- term:
    id: GO:0042179
    label: nicotine biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000041
  review:
    summary: QPT_0 is a plausible nicotine-pathway candidate, but exact paralog assignment remains open.
    action: KEEP_AS_NON_CORE
    reason: >-
      Family-level and UniProt evidence keep QPT_0 in scope for the nicotine
      pyridine branch, yet the current data do not conclusively rank it above
      QPT_1 as the specialized root copy.
    supported_by:
    - reference_id: file:NICAT/NaQPT2_candidate_QPT_0/NaQPT2_candidate_QPT_0-notes.md
      supporting_text: QPT_0 is therefore a plausible NaQPT2 candidate, but the current public record does not by itself establish whether QPT_0 or QPT_1 is the root nicotine-pathway-specialized paralog.
      reference_section_type: LITERATURE_REVIEW
core_functions:
- molecular_function:
    id: GO:0004514
    label: nicotinate-nucleotide diphosphorylase (carboxylating) activity
  directly_involved_in:
  - id: GO:0009435
    label: NAD+ biosynthetic process
  - id: GO:0034213
    label: quinolinate catabolic process
  description: >-
    QPT_0 catalyzes the quinolinate phosphoribosyltransferase step of de novo NAD
    biosynthesis and is a plausible duplicated pyridine-branch contributor to
    nicotine biosynthesis.
  supported_by:
  - reference_id: file:NICAT/NaQPT2_candidate_QPT_0/NaQPT2_candidate_QPT_0-notes.md
    supporting_text: UniProt curates A0A1J6KEF3 as nicotinate-nucleotide diphosphorylase (carboxylating), the quinolinate phosphoribosyltransferase/NadC reaction that connects quinolinate metabolism to NAD and nicotine pathway annotations.
    reference_section_type: LITERATURE_REVIEW
proposed_new_terms: []
suggested_questions:
- question: Which of the two QPT paralogs is most strongly coupled to nicotine induction and root-enriched pathway expression?
- question: Do QPT_0 and QPT_1 differ in catalytic efficiency or tissue distribution enough to explain pathway specialization?
suggested_experiments:
- description: Compare QPT_0 and QPT_1 enzymatic activity and transcript abundance across nicotine-inducing conditions in roots.
  experiment_type: comparative biochemistry and expression profiling
  hypothesis: One QPT paralog is specialized for the nicotine-associated pyridine branch.
- description: Perturb QPT_0 and QPT_1 individually and quantify quinolinate, nicotinate ribonucleotide, and nicotine levels in roots.
  experiment_type: genetics plus metabolite profiling
  hypothesis: The pathway-specialized QPT paralog will have a stronger effect on nicotine precursor supply.

NaQPT2_candidate_QPT_0

Gene Description