PMT1 is a root-expressed putrescine N-methyltransferase from Nicotiana attenuata that commits polyamine flux into the pyrrolidine branch of nicotine biosynthesis by converting putrescine to N-methylputrescine. It is part of an inducible anti-herbivore defense pathway whose transcript abundance rises after jasmonate treatment, wounding, and Manduca sexta feeding, while ethylene suppresses that induction.
The preferred accession for this review is Q93XQ5. These relationships are manually assessed.
REFERENCE PROTEOME CANDIDATE · Reviewed 2026-10-19
Reference proteome: UP000187609
Retain Q93XQ5 as the primary Swiss-Prot accession. The leading sequence differs by one residue across 388 residues, but the reference entry is reviewed PMT3 whereas the primary is PMT1. Near identity is insufficient to collapse duplicated PMT loci or resolve nomenclature. Retain a candidate pending genomic placement and reconciliation of PMT1/PMT3 naming.
MMseqs2 searched 32,918 sequences across UP000187609 at E <= 1e-5 and sensitivity 7.5, returning 8 hits. Every returned sequence was globally aligned using BLOSUM62 with gap-open -10 and extension -0.5. Scores and sequences for all 8 returned candidates are retained, with 8 detailed alignment files. The heuristic search does not establish genomic absence or unique locus identity.
file:NICAT/NaPMT1.1/NaPMT1.1-record-evidence.yaml
target_sequence_count: 32918
file:NICAT/NaPMT1.1/NaPMT1.1-record-evidence.yaml
candidate_count: 8
A0A314LG79: 387 identities across 388 global-alignment columns (99.7423% identity including gaps), 1 substitutions and 0 gap columns. Query coverage is 100.0%; target coverage is 100.0%. Sequence similarity is interpreted in the manual rationale. Identity over paired residues is 99.7423% (387/388); gap columns are excluded from this denominator.
file:NICAT/NaPMT1.1/NaPMT1.1-record-evidence.yaml
query_length: 388 target_length: 388 alignment_columns: 388 identities: 387 mismatches: 1 gap_columns: 0 identity_percent: 99.7423 query_coverage_percent: 100.0 target_coverage_percent: 100.0
The primary accession is outside every searched exact-taxon reference proteome. Current UniProt records place A0A314LG79 in UP000187609 and give it the same taxon as the primary.
file:NICAT/NaPMT1.1/NaPMT1.1-record-evidence.yaml
primary_in_any_reference_proteome: false
file:NICAT/NaPMT1.1/NaPMT1.1-record-evidence.yaml
alternative_in_reference_proteome: true
file:NICAT/NaPMT1.1/NaPMT1.1-record-evidence.yaml
same_taxon: true
Sampled UniSave observations: 09-DEC-2015, entry version 59.: no Proteomes cross-reference; 12-AUG-2020, entry version 71.: no Proteomes cross-reference; 27-NOV-2024, entry version 81.: no Proteomes cross-reference. These dated observations do not establish uninterrupted membership/absence, the exact change date, or UniProt's motivation.
file:NICAT/NaPMT1.1/NaPMT1.1-record-evidence.yaml
entry_date: 09-DEC-2015, entry version 59. proteomes: []
file:NICAT/NaPMT1.1/NaPMT1.1-record-evidence.yaml
entry_date: 12-AUG-2020, entry version 71. proteomes: []
file:NICAT/NaPMT1.1/NaPMT1.1-record-evidence.yaml
entry_date: 27-NOV-2024, entry version 81. proteomes: []
The two reviewed entries are named PMT1 and PMT3; gene nomenclature and possible duplication remain unresolved despite near-identical sequence.
file:NICAT/NaPMT1.1/NaPMT1.1-record-evidence.yaml
value: PMT1
file:NICAT/NaPMT1.1/NaPMT1.1-record-evidence.yaml
value: PMT3
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003824 catalytic activity | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: This annotation is true but uninformative for PMT1. A specific catalytic term is already present for this enzyme. Reason: GO:0030750 putrescine N-methyltransferase activity captures the actual chemistry; the generic catalytic parent term adds no useful biological resolution. Supporting Evidence: file:NICAT/NaPMT1.1/NaPMT1.1-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 annotation is not the current catalytic activity of PMT1. It reflects homology to the ancestral spermidine synthase family rather than the specialized methyltransferase activity of this nicotine-pathway enzyme. Reason: Distinct chemistry, not merely a less specific term. GO:0004766 is defined as S-adenosylmethioninamine + putrescine = 5'-methylthioadenosine + spermidine, an aminopropyl transfer from decarboxylated SAM (EC 2.5.1.16). PMT1 catalyzes putrescine + S-adenosyl-L-methionine = N-methylputrescine + S-adenosyl-L- homocysteine (EC 2.1.1.53, RHEA:15037): a methyl transfer from undecarboxylated SAM giving a different product. PMT arose by duplication of spermidine synthase and retains the fold (Pfam PF01564/PF17284), which is why the family-level PTN node carries the ancestral term, but PANTHER's own subfamily assignment for this protein is PTHR11558:SF53 PUTRESCINE N-METHYLTRANSFERASE 1. The specific activity is already annotated as GO:0030750. Supporting Evidence: file:NICAT/NaPMT1.1/NaPMT1.1-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 this soluble pathway enzyme, but it is peripheral to the main curated claims for PMT1. Reason: The available evidence reviewed here strongly supports catalytic role, pathway placement, and root induction. The cytosol term is reasonable but not central enough to elevate as a core conclusion in this pass. |
| GO:0008295 spermidine biosynthetic process | IEA GO_REF:0000118 | REMOVE | Summary: This process annotation is incorrect for PMT1. The enzyme directs putrescine into nicotine alkaloid biosynthesis rather than into spermidine biosynthesis. Reason: Spermidine is not a product of PMT1. The enzyme's output is N-methylputrescine (EC 2.1.1.53), the first committed pyrrolidine-branch intermediate of nicotine biosynthesis, and UniProt places the protein in the nicotine pathway rather than in polyamine biosynthesis. Making spermidine requires the aminopropyl transfer that PMT1 no longer performs, so this is not a broad-but-true parent of the real process but a different pathway inherited from the spermidine-synthase ancestor at the PANTHER family node. GO:0042179 nicotine biosynthetic process carries the correct process assignment. Supporting Evidence: file:NICAT/NaPMT1.1/NaPMT1.1-notes.md PMT catalyzes S-adenosylmethionine-dependent methylation of putrescine to N-methylputrescine, the first specific metabolite on the route to nicotine. file:NICAT/NaPMT1.1/NaPMT1.1-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 PMT1, but it is regulatory context rather than the core biochemical role of the enzyme. Reason: PMT1 transcripts rise after methyl jasmonate treatment in the herbivory defense program, which justifies retaining the annotation without treating it as a core function. Supporting Evidence: file:NICAT/NaPMT1.1/NaPMT1.1-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 PMT1 and the best available GO term for its catalytic role. Reason: PMT1 catalyzes S-adenosylmethionine-dependent methylation of putrescine to form N-methylputrescine. Supporting Evidence: file:NICAT/NaPMT1.1/NaPMT1.1-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 biological-process annotation for PMT1. N-methylputrescine formation is an early committed step in nicotine biosynthesis. Reason: PMT1 channels putrescine into the nicotine pathway by generating the first dedicated pyrrolidine-branch intermediate. Supporting Evidence: file:NICAT/NaPMT1.1/NaPMT1.1-notes.md PMT catalyzes S-adenosylmethionine-dependent methylation of putrescine to N-methylputrescine, the first specific metabolite on the route to nicotine. file:NICAT/NaPMT1.1/NaPMT1.1-notes.md UniProt curates Q93XQ5 as Putrescine N-methyltransferase 1 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: PMT1 is part of a wound-inducible defense program, but this is context-level biology rather than its defining enzymatic function. Reason: The 2001 N. attenuata study supports wound-responsive transcript induction, so the annotation should be preserved as non-core. Supporting Evidence: file:NICAT/NaPMT1.1/NaPMT1.1-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: This annotation is supported by herbivory-induced PMT transcript accumulation, but it is not part of the catalytic core function. Reason: PMT1 participates in a defense response to Manduca sexta herbivory through inducible expression linked to nicotine production. Supporting Evidence: file:NICAT/NaPMT1.1/NaPMT1.1-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 evidence supports jasmonate-responsive expression of PMT1, but this should remain a contextual non-core annotation. Reason: The same study that cloned PMT1 showed strong MeJA-induced transcript accumulation, supporting the response annotation without changing the core pathway-centric interpretation of the gene. Supporting Evidence: file:NICAT/NaPMT1.1/NaPMT1.1-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. |
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Download this section (compressed HTML)Q: Are PMT1 and PMT2 biochemically interchangeable in vivo, or do they make distinct quantitative contributions to nicotine production under herbivory?
Q: Does the more weakly characterized PMT3 paralog contribute measurable catalytic flux to the nicotine pathway, or is it a noncore duplicate?
Experiment: Generate clean PMT1, PMT2, and double-loss lines in Nicotiana attenuata and quantify N-methylputrescine and nicotine after methyl jasmonate treatment and Manduca sexta feeding.
Hypothesis: PMT1 and PMT2 jointly provide the dominant committed methyltransferase activity for inducible nicotine biosynthesis.
Type: genetic perturbation plus metabolite profiling
Experiment: Compare recombinant PMT1 and PMT2 kinetic parameters with putrescine and related diamines to test whether the paralogs are catalytically redundant or subtly specialized.
Hypothesis: The two root PMT paralogs retain the same core activity but may differ in catalytic efficiency or inducible pathway contribution.
Type: biochemical enzyme assay
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