PMT2 is a root-expressed putrescine N-methyltransferase paralog from Nicotiana attenuata that converts putrescine to N-methylputrescine for the pyrrolidine branch of nicotine biosynthesis. Like PMT1, it is embedded in the inducible nicotine defense program and shows jasmonate-, wound-, and herbivory-responsive transcript accumulation.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0003824
catalytic activity
|
IEA
GO_REF:0000002 |
MARK AS OVER ANNOTATED |
Summary: This annotation is correct only at a very generic level and should not be treated as an informative curation outcome for PMT2.
Reason: GO:0030750 putrescine N-methyltransferase activity already captures the actual chemistry performed by PMT2.
Supporting Evidence:
file:NICAT/NaPMT1.2/NaPMT1.2-notes.md
PMT catalyzes S-adenosylmethionine-dependent methylation of putrescine to N-methylputrescine, the first specific metabolite on the route to nicotine.
|
|
GO:0004766
spermidine synthase activity
|
IEA
GO_REF:0000118 |
REMOVE |
Summary: This TreeGrafter assignment is a family-level miscall and should not be kept as the catalytic function of PMT2.
Reason: PMT2 belongs to a lineage derived from spermidine synthase but now performs specialized methyltransferase chemistry in nicotine biosynthesis.
Supporting Evidence:
file:NICAT/NaPMT1.2/NaPMT1.2-notes.md
TreeGrafter assignment to spermidine synthase reflects PMT's evolutionary origin from spermidine synthase rather than its present catalytic activity.
|
|
GO:0005829
cytosol
|
IEA
GO_REF:0000118 |
KEEP AS NON CORE |
Summary: Cytosolic localization is plausible for PMT2 but is not a major focus of the current literature-backed curation pass.
Reason: Retain the localization as a reasonable non-core inference while prioritizing the better-supported catalytic and pathway assignments.
|
|
GO:0008295
spermidine biosynthetic process
|
IEA
GO_REF:0000118 |
REMOVE |
Summary: This process annotation does not fit PMT2 biology. PMT2 contributes to nicotine alkaloid production, not spermidine biosynthesis.
Reason: The same family-level overtransfer that caused the spermidine synthase activity annotation also incorrectly projects PMT2 into the spermidine process.
Supporting Evidence:
file:NICAT/NaPMT1.2/NaPMT1.2-notes.md
PMT catalyzes S-adenosylmethionine-dependent methylation of putrescine to N-methylputrescine, the first specific metabolite on the route to nicotine.
file:NICAT/NaPMT1.2/NaPMT1.2-notes.md
TreeGrafter assignment to spermidine synthase reflects PMT's evolutionary origin from spermidine synthase rather than its present catalytic activity.
|
|
GO:0009753
response to jasmonic acid
|
IEA
GO_REF:0000117 |
KEEP AS NON CORE |
Summary: Jasmonate responsiveness is supported for PMT2, but it is better treated as regulatory context than as a core function.
Reason: MeJA induction is part of the defense program that controls PMT2 expression, yet the core role of the gene is catalytic entry into nicotine biosynthesis.
Supporting Evidence:
file:NICAT/NaPMT1.2/NaPMT1.2-notes.md
In N. attenuata, Winz and Baldwin cloned PMT1 and PMT2 and found that both root PMT transcripts rose after MeJA, wounding, and Manduca sexta herbivory, while ethylene suppressed this induction.
|
|
GO:0030750
putrescine N-methyltransferase activity
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: This is the core molecular function of PMT2 and accurately captures the enzyme's specialized chemistry.
Reason: PMT2 catalyzes S-adenosylmethionine-dependent methylation of putrescine to N-methylputrescine.
Supporting Evidence:
file:NICAT/NaPMT1.2/NaPMT1.2-notes.md
PMT catalyzes S-adenosylmethionine-dependent methylation of putrescine to N-methylputrescine, the first specific metabolite on the route to nicotine.
|
|
GO:0042179
nicotine biosynthetic process
|
IEA
GO_REF:0000041 |
ACCEPT |
Summary: This is an appropriate core pathway assignment for PMT2.
Reason: PMT2 generates the first dedicated pyrrolidine-branch intermediate and is part of the duplicated root nicotine pathway in N. attenuata.
Supporting Evidence:
file:NICAT/NaPMT1.2/NaPMT1.2-notes.md
PMT catalyzes S-adenosylmethionine-dependent methylation of putrescine to N-methylputrescine, the first specific metabolite on the route to nicotine.
file:NICAT/NaPMT1.2/NaPMT1.2-notes.md
UniProt curates Q93XQ4 as Putrescine N-methyltransferase 2 and places it in nicotine biosynthesis with predominant root expression.
|
|
GO:0009611
response to wounding
|
IEP
PMID:11299398 Molecular interactions between the specialist herbivore Mand... |
KEEP AS NON CORE |
Summary: Wound-responsive expression is supported for PMT2 but is ancillary to the gene's catalytic pathway role.
Reason: Retain the annotation as valid defense-response context without elevating it above the core enzymatic curation.
Supporting Evidence:
file:NICAT/NaPMT1.2/NaPMT1.2-notes.md
In N. attenuata, Winz and Baldwin cloned PMT1 and PMT2 and found that both root PMT transcripts rose after MeJA, wounding, and Manduca sexta herbivory, while ethylene suppressed this induction.
|
|
GO:0009625
response to insect
|
IEP
PMID:11299398 Molecular interactions between the specialist herbivore Mand... |
KEEP AS NON CORE |
Summary: PMT2 participates in insect-triggered defense induction, but that inducibility is not its central curated function.
Reason: Manduca sexta feeding induces PMT transcripts as part of nicotine defense, so the annotation should be preserved as a non-core context term.
Supporting Evidence:
file:NICAT/NaPMT1.2/NaPMT1.2-notes.md
In N. attenuata, Winz and Baldwin cloned PMT1 and PMT2 and found that both root PMT transcripts rose after MeJA, wounding, and Manduca sexta herbivory, while ethylene suppressed this induction.
|
|
GO:0009753
response to jasmonic acid
|
IEP
PMID:11299398 Molecular interactions between the specialist herbivore Mand... |
KEEP AS NON CORE |
Summary: The experimental annotation is supported, but the response term should remain explicitly non-core in this review.
Reason: MeJA induction helps explain defense regulation of PMT2 without changing the gene's primary biochemical interpretation.
Supporting Evidence:
file:NICAT/NaPMT1.2/NaPMT1.2-notes.md
In N. attenuata, Winz and Baldwin cloned PMT1 and PMT2 and found that both root PMT transcripts rose after MeJA, wounding, and Manduca sexta herbivory, while ethylene suppressed this induction.
|
Q: Are PMT1 and PMT2 dosage balanced in roots, or does one paralog dominate inducible nicotine flux under natural herbivory?
Q: How should PMT3 be classified relative to PMT1 and PMT2 once the core duplicated pathway members are fully reviewed?
Experiment: Measure nicotine-pathway metabolites and transcript compensation in PMT2 single-loss and PMT1 PMT2 double-loss lines before and after methyl jasmonate or Manduca sexta challenge.
Hypothesis: PMT2 contributes nonredundant but overlapping catalytic flux within the inducible root nicotine pathway.
Type: genetic perturbation plus metabolite profiling
Experiment: Reconstitute PMT2 biochemistry in vitro and compare catalytic efficiency and substrate preference directly against PMT1 using the same assay conditions.
Hypothesis: PMT2 retains core PMT chemistry but may differ quantitatively from PMT1 in kinetics or stability.
Type: biochemical enzyme assay
The expression of NaPMT1.2 is inducible by jasmonate signaling, a plant hormone pathway activated in response to herbivory and other stressors. Studies in related Nicotiana species have shown that jasmonate treatment upregulates PMT gene expression in roots, suggesting a conserved regulatory mechanism. This induction aligns with the plant's defense strategy, as increased nicotine production can deter herbivores. (pubmed.ncbi.nlm.nih.gov)
Evolutionary Context
PMT enzymes, including PMT2, are believed to have evolved from spermidine synthases, enzymes involved in polyamine biosynthesis. This evolutionary transition reflects a functional shift from general polyamine metabolism to specialized secondary metabolism, enabling the production of defensive alkaloids like nicotine. The structural and functional similarities between PMTs and spermidine synthases support this evolutionary relationship. (frontiersin.org)
Pathway Integration
Within the nicotine biosynthetic pathway, PMT2's activity is a critical control point. Following the formation of N-methylputrescine by PMT2, subsequent enzymatic steps lead to the production of nicotine. The regulation of PMT2, therefore, directly influences the flux through the pathway and the overall production of nicotine, highlighting its importance in the plant's chemical defense arsenal.
In summary, NaPMT1.2 encodes the enzyme PMT2, which catalyzes the methylation of putrescine to N-methylputrescine, initiating the nicotine biosynthetic pathway in Nicotiana attenuata. Its root-specific expression and inducibility by jasmonate signaling underscore its role in the plant's adaptive response to herbivory. The evolutionary derivation from spermidine synthases illustrates a functional adaptation toward specialized metabolism, emphasizing the enzyme's significance in plant defense mechanisms.
id: Q93XQ4
gene_symbol: PMT2
product_type: PROTEIN
status: DRAFT
aliases:
- NaPMT1.2
- NaPMT2
- Putrescine N-methyltransferase 2
taxon:
id: NCBITaxon:49451
label: Nicotiana attenuata
description: >-
PMT2 is a root-expressed putrescine N-methyltransferase paralog from Nicotiana
attenuata that converts putrescine to N-methylputrescine for the pyrrolidine
branch of nicotine biosynthesis. Like PMT1, it is embedded in the inducible
nicotine defense program and shows jasmonate-, wound-, and herbivory-responsive
transcript accumulation.
existing_annotations:
- term:
id: GO:0003824
label: catalytic activity
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: >-
This annotation is correct only at a very generic level and should not be
treated as an informative curation outcome for PMT2.
action: MARK_AS_OVER_ANNOTATED
reason: >-
GO:0030750 putrescine N-methyltransferase activity already captures the
actual chemistry performed by PMT2.
supported_by:
- reference_id: file:NICAT/NaPMT1.2/NaPMT1.2-notes.md
supporting_text: PMT catalyzes S-adenosylmethionine-dependent methylation of putrescine to N-methylputrescine, the first specific metabolite on the route to nicotine.
reference_section_type: LITERATURE_REVIEW
- term:
id: GO:0004766
label: spermidine synthase activity
evidence_type: IEA
original_reference_id: GO_REF:0000118
review:
summary: >-
This TreeGrafter assignment is a family-level miscall and should not be kept
as the catalytic function of PMT2.
action: REMOVE
reason: >-
PMT2 belongs to a lineage derived from spermidine synthase but now performs
specialized methyltransferase chemistry in nicotine biosynthesis.
supported_by:
- reference_id: file:NICAT/NaPMT1.2/NaPMT1.2-notes.md
supporting_text: TreeGrafter assignment to spermidine synthase reflects PMT's evolutionary origin from spermidine synthase rather than its present catalytic activity.
reference_section_type: LITERATURE_REVIEW
- term:
id: GO:0005829
label: cytosol
evidence_type: IEA
original_reference_id: GO_REF:0000118
review:
summary: >-
Cytosolic localization is plausible for PMT2 but is not a major focus of the
current literature-backed curation pass.
action: KEEP_AS_NON_CORE
reason: >-
Retain the localization as a reasonable non-core inference while prioritizing
the better-supported catalytic and pathway assignments.
- term:
id: GO:0008295
label: spermidine biosynthetic process
evidence_type: IEA
original_reference_id: GO_REF:0000118
review:
summary: >-
This process annotation does not fit PMT2 biology. PMT2 contributes to
nicotine alkaloid production, not spermidine biosynthesis.
action: REMOVE
reason: >-
The same family-level overtransfer that caused the spermidine synthase
activity annotation also incorrectly projects PMT2 into the spermidine
process.
supported_by:
- reference_id: file:NICAT/NaPMT1.2/NaPMT1.2-notes.md
supporting_text: PMT catalyzes S-adenosylmethionine-dependent methylation of putrescine to N-methylputrescine, the first specific metabolite on the route to nicotine.
reference_section_type: LITERATURE_REVIEW
- reference_id: file:NICAT/NaPMT1.2/NaPMT1.2-notes.md
supporting_text: TreeGrafter assignment to spermidine synthase reflects PMT's evolutionary origin from spermidine synthase rather than its present catalytic activity.
reference_section_type: LITERATURE_REVIEW
- term:
id: GO:0009753
label: response to jasmonic acid
evidence_type: IEA
original_reference_id: GO_REF:0000117
review:
summary: >-
Jasmonate responsiveness is supported for PMT2, but it is better treated as
regulatory context than as a core function.
action: KEEP_AS_NON_CORE
reason: >-
MeJA induction is part of the defense program that controls PMT2 expression,
yet the core role of the gene is catalytic entry into nicotine biosynthesis.
supported_by:
- reference_id: file:NICAT/NaPMT1.2/NaPMT1.2-notes.md
supporting_text: In N. attenuata, Winz and Baldwin cloned PMT1 and PMT2 and found that both root PMT transcripts rose after MeJA, wounding, and Manduca sexta herbivory, while ethylene suppressed this induction.
reference_section_type: LITERATURE_REVIEW
- term:
id: GO:0030750
label: putrescine N-methyltransferase activity
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: >-
This is the core molecular function of PMT2 and accurately captures the
enzyme's specialized chemistry.
action: ACCEPT
reason: >-
PMT2 catalyzes S-adenosylmethionine-dependent methylation of putrescine to
N-methylputrescine.
supported_by:
- reference_id: file:NICAT/NaPMT1.2/NaPMT1.2-notes.md
supporting_text: PMT catalyzes S-adenosylmethionine-dependent methylation of putrescine to N-methylputrescine, the first specific metabolite on the route to nicotine.
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 core pathway assignment for PMT2.
action: ACCEPT
reason: >-
PMT2 generates the first dedicated pyrrolidine-branch intermediate and is
part of the duplicated root nicotine pathway in N. attenuata.
supported_by:
- reference_id: file:NICAT/NaPMT1.2/NaPMT1.2-notes.md
supporting_text: PMT catalyzes S-adenosylmethionine-dependent methylation of putrescine to N-methylputrescine, the first specific metabolite on the route to nicotine.
reference_section_type: LITERATURE_REVIEW
- reference_id: file:NICAT/NaPMT1.2/NaPMT1.2-notes.md
supporting_text: UniProt curates Q93XQ4 as Putrescine N-methyltransferase 2 and places it in nicotine biosynthesis with predominant root expression.
reference_section_type: LITERATURE_REVIEW
- term:
id: GO:0009611
label: response to wounding
evidence_type: IEP
original_reference_id: PMID:11299398
review:
summary: >-
Wound-responsive expression is supported for PMT2 but is ancillary to the
gene's catalytic pathway role.
action: KEEP_AS_NON_CORE
reason: >-
Retain the annotation as valid defense-response context without elevating it
above the core enzymatic curation.
supported_by:
- reference_id: file:NICAT/NaPMT1.2/NaPMT1.2-notes.md
supporting_text: In N. attenuata, Winz and Baldwin cloned PMT1 and PMT2 and found that both root PMT transcripts rose after MeJA, wounding, and Manduca sexta herbivory, while ethylene suppressed this induction.
reference_section_type: LITERATURE_REVIEW
- term:
id: GO:0009625
label: response to insect
evidence_type: IEP
original_reference_id: PMID:11299398
review:
summary: >-
PMT2 participates in insect-triggered defense induction, but that
inducibility is not its central curated function.
action: KEEP_AS_NON_CORE
reason: >-
Manduca sexta feeding induces PMT transcripts as part of nicotine defense,
so the annotation should be preserved as a non-core context term.
supported_by:
- reference_id: file:NICAT/NaPMT1.2/NaPMT1.2-notes.md
supporting_text: In N. attenuata, Winz and Baldwin cloned PMT1 and PMT2 and found that both root PMT transcripts rose after MeJA, wounding, and Manduca sexta herbivory, while ethylene suppressed this induction.
reference_section_type: LITERATURE_REVIEW
- term:
id: GO:0009753
label: response to jasmonic acid
evidence_type: IEP
original_reference_id: PMID:11299398
review:
summary: >-
The experimental annotation is supported, but the response term should remain
explicitly non-core in this review.
action: KEEP_AS_NON_CORE
reason: >-
MeJA induction helps explain defense regulation of PMT2 without changing the
gene's primary biochemical interpretation.
supported_by:
- reference_id: file:NICAT/NaPMT1.2/NaPMT1.2-notes.md
supporting_text: In N. attenuata, Winz and Baldwin cloned PMT1 and PMT2 and found that both root PMT transcripts rose after MeJA, wounding, and Manduca sexta herbivory, while ethylene suppressed this induction.
reference_section_type: LITERATURE_REVIEW
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/NaPMT1.2/NaPMT1.2-uniprot.txt
title: UniProt entry Q93XQ4 for Nicotiana attenuata PMT2
findings:
- statement: UniProt identifies Q93XQ4 as Putrescine N-methyltransferase 2
supporting_text: 'DE RecName: Full=Putrescine N-methyltransferase 2'
reference_section_type: DATABASE_ENTRY
- statement: UniProt assigns PMT2 to nicotine biosynthesis
supporting_text: 'CC -!- PATHWAY: Alkaloid biosynthesis; nicotine biosynthesis.'
reference_section_type: DATABASE_ENTRY
- statement: UniProt reports predominant root expression for PMT2
supporting_text: 'CC -!- TISSUE SPECIFICITY: Mainly expressed in roots.'
reference_section_type: DATABASE_ENTRY
- id: file:NICAT/NaPMT1.2/NaPMT1.2-notes.md
title: NaPMT1.2 literature review notes
findings:
- statement: PMT2 is the reviewed Nicotiana attenuata PMT2 pathway enzyme
supporting_text: UniProt curates Q93XQ4 as Putrescine N-methyltransferase 2 and places it in nicotine biosynthesis with predominant root expression.
reference_section_type: LITERATURE_REVIEW
- statement: PMT2 carries out the first dedicated pyrrolidine-branch step toward nicotine
supporting_text: PMT catalyzes S-adenosylmethionine-dependent methylation of putrescine to N-methylputrescine, the first specific metabolite on the route to nicotine.
reference_section_type: LITERATURE_REVIEW
- statement: Spermidine synthase annotations on PMT2 are evolutionary-family overcalls
supporting_text: TreeGrafter assignment to spermidine synthase reflects PMT's evolutionary origin from spermidine synthase rather than its present catalytic activity.
reference_section_type: LITERATURE_REVIEW
- statement: PMT2 is part of jasmonate-, wound-, and herbivory-inducible nicotine defense
supporting_text: In N. attenuata, Winz and Baldwin cloned PMT1 and PMT2 and found that both root PMT transcripts rose after MeJA, wounding, and Manduca sexta herbivory, while ethylene suppressed this induction.
reference_section_type: LITERATURE_REVIEW
- statement: PMT2 fits the duplicated root nicotine pathway described in the Nicotiana genome study
supporting_text: The 2017 Nicotiana genome paper places root nicotine biosynthesis in N. attenuata as a duplicated specialization of polyamine and NAD metabolism, consistent with PMT as a root defense-pathway enzyme.
reference_section_type: LITERATURE_REVIEW
- id: PMID:11299398
title: Molecular interactions between the specialist herbivore Manduca sexta (Lepidoptera, Sphingidae) and its natural host Nicotiana attenuata. IV. Insect-Induced ethylene reduces jasmonate-induced nicotine accumulation by regulating putrescine N-methyltransferase transcripts.
findings:
- statement: PMT1 and PMT2 were cloned from Nicotiana attenuata as likely rate-limiting nicotine-pathway genes
supporting_text: we cloned the putrescine methyltransferase genes (NaPMT1 and NaPMT2) of N. attenuata, which are thought to represent the rate limiting step in nicotine biosynthesis
reference_section_type: ABSTRACT
- statement: Root PMT transcripts increase after methyl jasmonate treatment
supporting_text: Transcripts of both root putrescine N-methyltransferase (PMT) genes and nicotine accumulation increased dramatically within 10 h of shoot MeJA treatment
reference_section_type: ABSTRACT
- statement: Wounding and Manduca sexta herbivory elevate PMT transcript accumulation
supporting_text: 1-MCP pretreatment dramatically amplified the transcript accumulation resulting from both wounding and M. sexta herbivory
reference_section_type: ABSTRACT
- id: PMID:19651420
title: Putrescine N-methyltransferase--the start for alkaloids.
findings:
- statement: PMT catalyzes S-adenosylmethionine-dependent methylation of putrescine
supporting_text: Putrescine N-methyltransferase (PMT) catalyses S-adenosylmethionine (SAM) dependent methylation of the diamine putrescine.
reference_section_type: ABSTRACT
- statement: N-methylputrescine is the first specific metabolite on the route to nicotine
supporting_text: The product N-methylputrescine is the first specific metabolite on the route to nicotine, tropane, and nortropane alkaloids.
reference_section_type: ABSTRACT
- statement: PMT evolved from plant spermidine synthase
supporting_text: PMT is likely to have evolved from the ubiquitous enzyme spermidine synthase.
reference_section_type: ABSTRACT
- id: PMID:28536194
title: Wild tobacco genomes reveal the evolution of nicotine biosynthesis.
findings:
- statement: Root nicotine biosynthesis in Nicotiana evolved from duplicated polyamine and NAD pathways
supporting_text: 'The biosynthetic machinery that allows for nicotine synthesis in the roots evolved from the stepwise duplications of two ancient primary metabolic pathways: the polyamine and nicotinamide adenine dinucleotide (NAD) pathways.'
reference_section_type: ABSTRACT
core_functions:
- molecular_function:
id: GO:0030750
label: putrescine N-methyltransferase activity
directly_involved_in:
- id: GO:0042179
label: nicotine biosynthetic process
description: >-
PMT2 catalyzes the S-adenosylmethionine-dependent methylation of putrescine
to N-methylputrescine, providing the same committed pyrrolidine-branch entry
chemistry as PMT1 within the duplicated Nicotiana attenuata root nicotine
pathway.
supported_by:
- reference_id: file:NICAT/NaPMT1.2/NaPMT1.2-notes.md
supporting_text: PMT catalyzes S-adenosylmethionine-dependent methylation of putrescine to N-methylputrescine, the first specific metabolite on the route to nicotine.
reference_section_type: LITERATURE_REVIEW
- reference_id: file:NICAT/NaPMT1.2/NaPMT1.2-notes.md
supporting_text: The 2017 Nicotiana genome paper places root nicotine biosynthesis in N. attenuata as a duplicated specialization of polyamine and NAD metabolism, consistent with PMT as a root defense-pathway enzyme.
reference_section_type: LITERATURE_REVIEW
proposed_new_terms: []
suggested_questions:
- question: Are PMT1 and PMT2 dosage balanced in roots, or does one paralog dominate inducible nicotine flux under natural herbivory?
- question: How should PMT3 be classified relative to PMT1 and PMT2 once the core duplicated pathway members are fully reviewed?
suggested_experiments:
- description: Measure nicotine-pathway metabolites and transcript compensation in PMT2 single-loss and PMT1 PMT2 double-loss lines before and after methyl jasmonate or Manduca sexta challenge.
experiment_type: genetic perturbation plus metabolite profiling
hypothesis: PMT2 contributes nonredundant but overlapping catalytic flux within the inducible root nicotine pathway.
- description: Reconstitute PMT2 biochemistry in vitro and compare catalytic efficiency and substrate preference directly against PMT1 using the same assay conditions.
experiment_type: biochemical enzyme assay
hypothesis: PMT2 retains core PMT chemistry but may differ quantitatively from PMT1 in kinetics or stability.