Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0004514 nicotinate-nucleotide diphosphorylase (carboxylating) activity	IEA GO_REF:0000120	ACCEPT	Summary: This is the correct catalytic activity for QPT_1. Reason: The accession is consistently identified as a quinolinate phosphoribosyltransferase family protein. Supporting Evidence: file:NICAT/NaQPT2_candidate_QPT_1/NaQPT2_candidate_QPT_1-notes.md UniProt curates A0A1J6IKI8 as nicotinate-nucleotide diphosphorylase (carboxylating), the quinolinate phosphoribosyltransferase/NadC chemistry that links quinolinate to NAD and nicotine pathway annotations.
GO:0005737 cytoplasm	IEA GO_REF:0000118	KEEP AS NON CORE	Summary: Cytoplasmic localization is reasonable but peripheral. Reason: This location is plausible for QPT chemistry, but the important unresolved issue is whether QPT_1 is the pathway-specialized paralog.
GO:0009435 NAD+ biosynthetic process	IEA GO_REF:0000120	ACCEPT	Summary: QPT_1 belongs in NAD biosynthesis. Reason: This step converts quinolinate into a de novo NAD precursor and therefore clearly belongs in the NAD pathway. Supporting Evidence: file:NICAT/NaQPT2_candidate_QPT_1/NaQPT2_candidate_QPT_1-notes.md UniProt curates A0A1J6IKI8 as nicotinate-nucleotide diphosphorylase (carboxylating), the quinolinate phosphoribosyltransferase/NadC chemistry that links quinolinate to NAD and nicotine pathway annotations.
GO:0009611 response to wounding	IEA GO_REF:0000117	KEEP AS NON CORE	Summary: This automated response term is plausible but not a core conclusion for QPT_1. Reason: Keep the annotation as a contextual inference rather than a central functional claim for this candidate.
GO:0016763 pentosyltransferase activity	IEA GO_REF:0000002	MODIFY	Summary: This is too broad relative to the specific catalytic activity already assigned. Reason: QPT_1 has a specific phosphoribosyltransferase annotation that should be preferred over the generic pentosyltransferase parent. Proposed replacements: nicotinate-nucleotide diphosphorylase (carboxylating) activity
GO:0034213 quinolinate catabolic process	IEA GO_REF:0000118	ACCEPT	Summary: This process term fits QPT_1 well. Reason: QPT chemistry consumes quinolinate and therefore belongs in quinolinate catabolism.
GO:0042179 nicotine biosynthetic process	IEA GO_REF:0000041	KEEP AS NON CORE	Summary: QPT_1 is a plausible nicotine-pathway paralog, but the exact specialized copy remains unresolved. Reason: Family-level evidence and current UniProt annotation keep QPT_1 in scope, yet the available data still do not discriminate decisively between QPT_1 and QPT_0. Supporting Evidence: file:NICAT/NaQPT2_candidate_QPT_1/NaQPT2_candidate_QPT_1-notes.md QPT_1 remains a plausible NaQPT2 candidate, but the public annotations alone do not resolve whether it is the pathway-specialized copy versus QPT_0.

Core Functions

QPT_1 catalyzes the quinolinate phosphoribosyltransferase step in de novo NAD biosynthesis and remains a plausible nicotine-associated QPT paralog.

Molecular Function:

nicotinate-nucleotide diphosphorylase (carboxylating) activity

Directly Involved In:

NAD+ biosynthetic process quinolinate catabolic process

Supporting Evidence:

file:NICAT/NaQPT2_candidate_QPT_1/NaQPT2_candidate_QPT_1-notes.md
UniProt curates A0A1J6IKI8 as nicotinate-nucleotide diphosphorylase (carboxylating), the quinolinate phosphoribosyltransferase/NadC chemistry that links quinolinate 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_1/NaQPT2_candidate_QPT_1-uniprot.txt

UniProt entry A0A1J6IKI8 for Nicotiana attenuata QPT_1

QPT_1 is a quinolinate phosphoribosyltransferase family enzyme

"DE RecName: Full=nicotinate-nucleotide diphosphorylase (carboxylating)"
UniProt places QPT_1 in both NAD and nicotine pathway annotations

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

file:NICAT/NaQPT2_candidate_QPT_1/NaQPT2_candidate_QPT_1-notes.md

NaQPT2 QPT_1 candidate notes

QPT_1 is a credible duplicated pyridine-branch candidate

"UniProt curates A0A1J6IKI8 as nicotinate-nucleotide diphosphorylase (carboxylating), the quinolinate phosphoribosyltransferase/NadC chemistry that links quinolinate to NAD and nicotine pathway annotations."
QPT_1 remains unresolved relative to QPT_0 for pathway specialization

"QPT_1 remains a plausible NaQPT2 candidate, but the public annotations alone do not resolve whether it is the pathway-specialized copy versus QPT_0."

Suggested Experiments

Experiment: Compare QPT_1 and QPT_0 catalytic properties and induction patterns under nicotine-promoting conditions.

Hypothesis: One QPT paralog is more tightly coupled to defense-associated nicotine biosynthesis.

Type: comparative biochemistry and expression profiling

Experiment: Measure the effect of selective QPT_1 disruption on NAD precursors and nicotine accumulation in roots.

Hypothesis: If QPT_1 is the specialized paralog, its loss will measurably reduce nicotine precursor flux.

Type: genetics plus metabolite profiling

Deep Research

OpenAI

(NaQPT2_candidate_QPT_1-deep-research-openai.md)

**Catalytic Activity:** OpenAI gpt-4.1 1 citations 2026-04-05T13:08:37.130985

The protein encoded by the gene NaQPT2_candidate_QPT_1 in Nicotiana attenuata is identified as nicotinate-nucleotide diphosphorylase (carboxylating), also known as quinolinate phosphoribosyltransferase (QAPRTase). This enzyme plays a pivotal role in the biosynthesis of nicotinamide adenine dinucleotide (NAD⁺), a crucial coenzyme in cellular metabolism.

Catalytic Activity:

The enzyme catalyzes the conversion of quinolinate (pyridine-2,3-dicarboxylate) to nicotinate D-ribonucleotide (NaMN), a key intermediate in the NAD⁺ biosynthetic pathway. The reaction proceeds as follows:

[ \text{Quinolinate} + 5\text{-phospho-}\alpha\text{-D-ribose 1-diphosphate} \rightarrow \text{Nicotinate D-ribonucleotide} + \text{CO}_2 + \text{Diphosphate} ]

This reaction is essential for the de novo synthesis of NAD⁺, facilitating the conversion of quinolinate, derived from tryptophan metabolism, into NaMN. The enzyme's activity is classified under EC 2.4.2.19. (enzyme.expasy.org)

Biological Process:

In plants, NAD⁺ is vital for various metabolic processes, including glycolysis, the tricarboxylic acid cycle, and oxidative phosphorylation. The biosynthesis of NAD⁺ through the de novo pathway, involving QAPRTase, is crucial for maintaining cellular redox balance and energy metabolism.

3. Structural and Domain Information

The protein belongs to the NadC/ModD family and contains several conserved domains:

Aldolase_TIM (IPR013785): A domain associated with the TIM barrel fold, common in enzymes with diverse catalytic functions.
NadC (IPR004393): A domain specific to nicotinate-nucleotide diphosphorylases, indicating its role in NAD⁺ biosynthesis.
NadC/ModD (IPR027277): A superfamily domain encompassing enzymes involved in NAD⁺ biosynthesis.
Nicotinate_pribotase-like_C (IPR036068): A C-terminal domain found in nicotinate phosphoribosyltransferases.
Quinolinate_PRibosylTase_N_sf (IPR037128): An N-terminal domain associated with quinolinate phosphoribosyltransferase activity.

These domains collectively contribute to the enzyme's function in catalyzing the conversion of quinolinate to NaMN.

4. Localization

While specific subcellular localization data for the Nicotiana attenuata QAPRTase is not available, similar enzymes in other organisms are typically localized in the cytoplasm, where NAD⁺ biosynthesis occurs. Therefore, it is reasonable to infer a cytoplasmic localization for this enzyme in Nicotiana attenuata.

5. Pathway Involvement

The enzyme is a key component of the de novo NAD⁺ biosynthesis pathway. In plants, this pathway is essential for producing NAD⁺ from quinolinate, derived from tryptophan metabolism. NAD⁺ serves as a coenzyme in redox reactions, playing a central role in energy metabolism and various biosynthetic processes.

6. Evolutionary Conservation

Nicotinate-nucleotide diphosphorylases are conserved across various species, including bacteria, archaea, and eukaryotes, indicating their fundamental role in cellular metabolism. The conservation of key domains and catalytic mechanisms underscores the enzyme's essential function in NAD⁺ biosynthesis.

7. Experimental Evidence and Inference

Direct experimental studies on the Nicotiana attenuata QAPRTase are limited. However, the presence of conserved domains and its classification within the NadC/ModD family strongly suggest that this enzyme performs a similar function to its homologs in other organisms. Bioinformatic analyses and comparative studies support this inference, highlighting the enzyme's role in NAD⁺ biosynthesis.

8. Conclusion

The NaQPT2_candidate_QPT_1 gene in Nicotiana attenuata encodes a nicotinate-nucleotide diphosphorylase (carboxylating) enzyme, integral to the de novo NAD⁺ biosynthesis pathway. Through the conversion of quinolinate to nicotinate D-ribonucleotide, this enzyme contributes to the production of NAD⁺, a coenzyme essential for numerous metabolic processes. While direct experimental data in Nicotiana attenuata is scarce, the conserved nature of this enzyme across species provides a strong basis for its functional annotation.

📚 Additional Documentation

Notes

(NaQPT2_candidate_QPT_1-notes.md)

NaQPT2_candidate_QPT_1 Notes

UniProt curates A0A1J6IKI8 as nicotinate-nucleotide diphosphorylase (carboxylating), the quinolinate phosphoribosyltransferase/NadC chemistry that links quinolinate to NAD and nicotine pathway annotations. [file:NICAT/NaQPT2_candidate_QPT_1/NaQPT2_candidate_QPT_1-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 assigns QPT_1 to the NadC/ModD family and to both NAD+ biosynthetic process and nicotine biosynthetic process, so it is also a credible pathway candidate rather than a generic unrelated transferase. [file:NICAT/NaQPT2_candidate_QPT_1/NaQPT2_candidate_QPT_1-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 attributes nicotine-pathway evolution in part to duplications within the NAD pathway, which is why both QPT_0 and QPT_1 deserve explicit paralog resolution. PMID:28536194
The full glucosylation preprint keeps QPT2 inside the coordinated nicotine gene set by placing it among the stronger tobacco genes correlated with UGT1, which supports continued QPT paralog review without resolving the NICAT split. [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_1 remains a plausible NaQPT2 candidate, but the public annotations alone do not resolve whether it is the pathway-specialized copy versus QPT_0. [file:NICAT/NaQPT2_candidate_QPT_1/NaQPT2_candidate_QPT_1-uniprot.txt "GN Name=QPT_1"; "CC -!- PATHWAY: Alkaloid biosynthesis; nicotine biosynthesis."]

📄 View Raw YAML

id: A0A1J6IKI8
gene_symbol: NaQPT2_candidate_QPT_1
product_type: PROTEIN
status: DRAFT
aliases:
- QPT_1
- NaQPT2
taxon:
  id: NCBITaxon:49451
  label: Nicotiana attenuata
description: >-
  NaQPT2_candidate_QPT_1 is the second current NICAT quinolinate
  phosphoribosyltransferase candidate in the duplicated pyridine branch of
  nicotine biosynthesis. Like QPT_0, it is a credible NAD-pathway enzyme and a
  plausible nicotine-associated paralog, but the specialized copy is not yet
  resolved.
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_1/NaQPT2_candidate_QPT_1-uniprot.txt
  title: UniProt entry A0A1J6IKI8 for Nicotiana attenuata QPT_1
  findings:
  - statement: QPT_1 is a quinolinate phosphoribosyltransferase family enzyme
    supporting_text: 'DE   RecName: Full=nicotinate-nucleotide diphosphorylase (carboxylating)'
    reference_section_type: DATABASE_ENTRY
  - statement: UniProt places QPT_1 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_1/NaQPT2_candidate_QPT_1-notes.md
  title: NaQPT2 QPT_1 candidate notes
  findings:
  - statement: QPT_1 is a credible duplicated pyridine-branch candidate
    supporting_text: UniProt curates A0A1J6IKI8 as nicotinate-nucleotide diphosphorylase (carboxylating), the quinolinate phosphoribosyltransferase/NadC chemistry that links quinolinate to NAD and nicotine pathway annotations.
    reference_section_type: LITERATURE_REVIEW
  - statement: QPT_1 remains unresolved relative to QPT_0 for pathway specialization
    supporting_text: QPT_1 remains a plausible NaQPT2 candidate, but the public annotations alone do not resolve whether it is the pathway-specialized copy versus QPT_0.
    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 correct catalytic activity for QPT_1.
    action: ACCEPT
    reason: >-
      The accession is consistently identified as a quinolinate
      phosphoribosyltransferase family protein.
    supported_by:
    - reference_id: file:NICAT/NaQPT2_candidate_QPT_1/NaQPT2_candidate_QPT_1-notes.md
      supporting_text: UniProt curates A0A1J6IKI8 as nicotinate-nucleotide diphosphorylase (carboxylating), the quinolinate phosphoribosyltransferase/NadC chemistry that links quinolinate 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 reasonable but peripheral.
    action: KEEP_AS_NON_CORE
    reason: >-
      This location is plausible for QPT chemistry, but the important unresolved
      issue is whether QPT_1 is the pathway-specialized paralog.
- term:
    id: GO:0009435
    label: NAD+ biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: QPT_1 belongs in NAD biosynthesis.
    action: ACCEPT
    reason: >-
      This step converts quinolinate into a de novo NAD precursor and therefore
      clearly belongs in the NAD pathway.
    supported_by:
    - reference_id: file:NICAT/NaQPT2_candidate_QPT_1/NaQPT2_candidate_QPT_1-notes.md
      supporting_text: UniProt curates A0A1J6IKI8 as nicotinate-nucleotide diphosphorylase (carboxylating), the quinolinate phosphoribosyltransferase/NadC chemistry that links quinolinate 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 automated response term is plausible but not a core conclusion for QPT_1.
    action: KEEP_AS_NON_CORE
    reason: >-
      Keep the annotation as a contextual inference rather than a central
      functional claim for this candidate.
- term:
    id: GO:0016763
    label: pentosyltransferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: This is too broad relative to the specific catalytic activity already assigned.
    action: MODIFY
    reason: >-
      QPT_1 has a specific phosphoribosyltransferase annotation that should be
      preferred over the generic pentosyltransferase parent.
    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 term fits QPT_1 well.
    action: ACCEPT
    reason: >-
      QPT chemistry consumes quinolinate and therefore belongs in quinolinate
      catabolism.
- term:
    id: GO:0042179
    label: nicotine biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000041
  review:
    summary: QPT_1 is a plausible nicotine-pathway paralog, but the exact specialized copy remains unresolved.
    action: KEEP_AS_NON_CORE
    reason: >-
      Family-level evidence and current UniProt annotation keep QPT_1 in scope,
      yet the available data still do not discriminate decisively between QPT_1
      and QPT_0.
    supported_by:
    - reference_id: file:NICAT/NaQPT2_candidate_QPT_1/NaQPT2_candidate_QPT_1-notes.md
      supporting_text: QPT_1 remains a plausible NaQPT2 candidate, but the public annotations alone do not resolve whether it is the pathway-specialized copy versus QPT_0.
      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_1 catalyzes the quinolinate phosphoribosyltransferase step in de novo NAD
    biosynthesis and remains a plausible nicotine-associated QPT paralog.
  supported_by:
  - reference_id: file:NICAT/NaQPT2_candidate_QPT_1/NaQPT2_candidate_QPT_1-notes.md
    supporting_text: UniProt curates A0A1J6IKI8 as nicotinate-nucleotide diphosphorylase (carboxylating), the quinolinate phosphoribosyltransferase/NadC chemistry that links quinolinate to NAD and nicotine pathway annotations.
    reference_section_type: LITERATURE_REVIEW
proposed_new_terms: []
suggested_questions:
- question: Does QPT_1 show stronger nicotine-pathway induction or root specificity than QPT_0?
- question: Are both QPT paralogs catalytically redundant, or has one specialized for defense-associated nicotine production?
suggested_experiments:
- description: Compare QPT_1 and QPT_0 catalytic properties and induction patterns under nicotine-promoting conditions.
  experiment_type: comparative biochemistry and expression profiling
  hypothesis: One QPT paralog is more tightly coupled to defense-associated nicotine biosynthesis.
- description: Measure the effect of selective QPT_1 disruption on NAD precursors and nicotine accumulation in roots.
  experiment_type: genetics plus metabolite profiling
  hypothesis: If QPT_1 is the specialized paralog, its loss will measurably reduce nicotine precursor flux.

NaQPT2_candidate_QPT_1

Gene Description