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.
| 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: PMT proteins evolved from spermidine synthase but catalyze S-adenosylmethionine-dependent methylation of putrescine, not spermidine synthesis. 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: PMT1 generates N-methylputrescine as a dedicated nicotine-pathway intermediate; the spermidine-process assignment is an ancestral family overcall. 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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