NaPMT3 is a root-expressed putrescine N-methyltransferase paralog in Nicotiana attenuata. It carries PMT-family methyltransferase chemistry and nicotine-pathway association, but PMT3 is less established than the better characterized PMT1.1 and PMT1.2 pair for core nicotine-pathway PMT function.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003824 catalytic activity | IEA GO_REF:0000002 | ACCEPT | Summary: NaPMT3 catalyzes SAM-dependent methyl transfer to putrescine. Reason: Catalytic activity is an entailed broad molecular function of the accepted putrescine N-methyltransferase activity. Its generality is not over-annotation. |
| GO:0004766 spermidine synthase activity | IEA GO_REF:0000118 | REMOVE | Summary: This is a family-origin overcall and should be removed. Reason: PMT proteins evolved from spermidine synthase but now catalyze putrescine N-methylation in alkaloid biosynthesis. The target carries the PMT-specific IPR025803/PROSITE assignment and the SAM-dependent methylation reaction. The existing reports support a PMT-versus-SPDS functional divergence, not loss of catalytic function. Supporting Evidence: file:NICAT/NaPMT3/NaPMT3-notes.md UniProt curates A0A314LG79 as Putrescine N-methyltransferase 3, assigns the reaction from putrescine to N-methylputrescine, places the protein in nicotine biosynthesis, and reports predominant root expression. file:NICAT/NaPMT3/NaPMT3-hypotheses/function-hypothesis-go-0004766/openscientist.md Verdict: Wrong subfamily (mis-placed) - Failure Mode 1 (Granularity / family-vs-subfamily error) file:NICAT/NaPMT3/NaPMT3-hypotheses/function-hypothesis-go-0004766/openscientist.md SAM-dependent methyl transfer (PMT) versus dcSAM-dependent aminopropyl transfer (SPDS) file:NICAT/NaPMT3/NaPMT3-hypotheses/function-hypothesis-go-0004766/falcon.md PMT transfers a methyl group from intact S-adenosylmethionine (SAM) to putrescine to form N-methylputrescine |
| GO:0005829 cytosol | IEA GO_REF:0000118 | ACCEPT | Summary: Cytosol is a reasonable conserved localization for this soluble PMT enzyme. Reason: The TreeGrafter localization is compatible with the PMT family and there is no target-specific evidence of a different compartment. Less detailed study of PMT3 than PMT1 does not make the same enzymatic location non-core. |
| GO:0008295 spermidine biosynthetic process | IEA GO_REF:0000118 | REMOVE | Summary: This process annotation reflects ancestral family membership rather than current function. Reason: PMT3 channels putrescine into alkaloid biosynthesis rather than spermidine biosynthesis. Supporting Evidence: file:NICAT/NaPMT3/NaPMT3-notes.md UniProt curates A0A314LG79 as Putrescine N-methyltransferase 3, assigns the reaction from putrescine to N-methylputrescine, places the protein in nicotine biosynthesis, and reports predominant root expression. |
| GO:0009753 response to jasmonic acid | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: Jasmonate responsiveness is plausible but should remain non-core. Reason: The annotation fits nicotine defense-pathway context but is less central than the catalytic and pathway assignments. |
| GO:0030750 putrescine N-methyltransferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: This is the core catalytic annotation for PMT3. Reason: UniProt explicitly assigns the putrescine methyltransferase reaction to this root-expressed paralog. Supporting Evidence: file:NICAT/NaPMT3/NaPMT3-notes.md UniProt curates A0A314LG79 as Putrescine N-methyltransferase 3, assigns the reaction from putrescine to N-methylputrescine, places the protein in nicotine biosynthesis, and reports predominant root expression. |
| GO:0042179 nicotine biosynthetic process | IEA GO_REF:0000041 | ACCEPT | Summary: NaPMT3 is a PMT paralog assigned to nicotine biosynthesis by conserved reaction and family evidence. Reason: UniProt assigns PMT3 to the putrescine-to-N-methylputrescine step of nicotine biosynthesis; its PMT-specific InterPro signature and root expression support that inference. Uncertainty about relative flux contribution compared with PMT1 paralogs does not make the same pathway activity non-core. Supporting Evidence: file:NICAT/NaPMT3/NaPMT3-notes.md The paper does not distinguish whether a PMT3-like paralog in NICAT is part of the core flux-carrying pair or a secondary duplicate, so PMT3 remains follow-up rather than an automatically accepted seed-core anchor. PMID:19651420 The product N-methylputrescine is the first specific metabolite on the route to nicotine, tropane, and nortropane alkaloids. |
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Download this section (compressed HTML)Q: Does PMT3 contribute measurable flux to nicotine biosynthesis, or is it a lower-priority duplicate relative to PMT1.1 and PMT1.2?
Q: Is PMT3 induced under the same defense conditions as the better characterized PMT paralogs?
Experiment: Compare PMT3, PMT1.1, and PMT1.2 catalytic activity and induction profiles after topping, jasmonate treatment, and herbivory.
Hypothesis: PMT3 is catalytically competent but contributes less flux than the canonical PMT pair.
Type: comparative biochemistry and expression profiling
Experiment: Measure N-methylputrescine and nicotine levels after selective PMT3 disruption in roots.
Hypothesis: PMT3 has a modest but detectable contribution to pyrrolidine-branch flux.
Type: genetic perturbation plus metabolite profiling
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