id: Q93XQ5 gene_symbol: PMT1 product_type: PROTEIN status: DRAFT aliases: - NaPMT1.1 - NaPMT1 - Putrescine N-methyltransferase 1 taxon: id: NCBITaxon:49451 label: Nicotiana attenuata description: >- 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. alternative_records: - id: A0A314LG79 relationship: REFERENCE_PROTEOME_CANDIDATE reference_proteome: UP000187609 reviewed_on: '2026-10-19' reason: 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. evidence: - type: PROTEOME_SEARCH description: 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. supported_by: - reference_id: file:NICAT/NaPMT1.1/NaPMT1.1-record-evidence.yaml supporting_text: 'target_sequence_count: 32918' - reference_id: file:NICAT/NaPMT1.1/NaPMT1.1-record-evidence.yaml supporting_text: 'candidate_count: 8' - type: SEQUENCE_COMPARISON description: '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.' supported_by: - reference_id: file:NICAT/NaPMT1.1/NaPMT1.1-record-evidence.yaml supporting_text: |- 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 - type: PROTEOME_MEMBERSHIP description: 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. supported_by: - reference_id: file:NICAT/NaPMT1.1/NaPMT1.1-record-evidence.yaml supporting_text: 'primary_in_any_reference_proteome: false' - reference_id: file:NICAT/NaPMT1.1/NaPMT1.1-record-evidence.yaml supporting_text: 'alternative_in_reference_proteome: true' - reference_id: file:NICAT/NaPMT1.1/NaPMT1.1-record-evidence.yaml supporting_text: 'same_taxon: true' - type: RECORD_HISTORY description: '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.' supported_by: - reference_id: file:NICAT/NaPMT1.1/NaPMT1.1-record-evidence.yaml supporting_text: |- entry_date: 09-DEC-2015, entry version 59. proteomes: [] - reference_id: file:NICAT/NaPMT1.1/NaPMT1.1-record-evidence.yaml supporting_text: |- entry_date: 12-AUG-2020, entry version 71. proteomes: [] - reference_id: file:NICAT/NaPMT1.1/NaPMT1.1-record-evidence.yaml supporting_text: |- entry_date: 27-NOV-2024, entry version 81. proteomes: [] - type: CURATION_CONTEXT description: The two reviewed entries are named PMT1 and PMT3; gene nomenclature and possible duplication remain unresolved despite near-identical sequence. supported_by: - reference_id: file:NICAT/NaPMT1.1/NaPMT1.1-record-evidence.yaml supporting_text: 'value: PMT1' - reference_id: file:NICAT/NaPMT1.1/NaPMT1.1-record-evidence.yaml supporting_text: 'value: PMT3' existing_annotations: - term: id: GO:0003824 label: catalytic activity evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: enables review: summary: >- This annotation is true but uninformative for PMT1. A specific catalytic term is already present for this enzyme. action: MARK_AS_OVER_ANNOTATED reason: >- GO:0030750 putrescine N-methyltransferase activity captures the actual chemistry; the generic catalytic parent term adds no useful biological resolution. supported_by: - reference_id: file:NICAT/NaPMT1.1/NaPMT1.1-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 qualifier: enables review: 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. action: REMOVE 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. supported_by: - reference_id: file:NICAT/NaPMT1.1/NaPMT1.1-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 qualifier: located_in review: summary: >- Cytosolic localization is plausible for this soluble pathway enzyme, but it is peripheral to the main curated claims for PMT1. action: KEEP_AS_NON_CORE 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. - term: id: GO:0008295 label: spermidine biosynthetic process evidence_type: IEA original_reference_id: GO_REF:0000118 qualifier: involved_in review: summary: >- This process annotation is incorrect for PMT1. The enzyme directs putrescine into nicotine alkaloid biosynthesis rather than into spermidine biosynthesis. action: REMOVE 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. supported_by: - reference_id: file:NICAT/NaPMT1.1/NaPMT1.1-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/NaPMT1.1/NaPMT1.1-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 qualifier: involved_in review: summary: >- Jasmonate responsiveness is supported for PMT1, but it is regulatory context rather than the core biochemical role of the enzyme. action: KEEP_AS_NON_CORE 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. supported_by: - reference_id: file:NICAT/NaPMT1.1/NaPMT1.1-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 qualifier: enables review: summary: >- This is the core molecular function of PMT1 and the best available GO term for its catalytic role. action: ACCEPT reason: >- PMT1 catalyzes S-adenosylmethionine-dependent methylation of putrescine to form N-methylputrescine. supported_by: - reference_id: file:NICAT/NaPMT1.1/NaPMT1.1-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 qualifier: involved_in review: summary: >- This is an appropriate core biological-process annotation for PMT1. N-methylputrescine formation is an early committed step in nicotine biosynthesis. action: ACCEPT reason: >- PMT1 channels putrescine into the nicotine pathway by generating the first dedicated pyrrolidine-branch intermediate. supported_by: - reference_id: file:NICAT/NaPMT1.1/NaPMT1.1-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/NaPMT1.1/NaPMT1.1-notes.md supporting_text: UniProt curates Q93XQ5 as Putrescine N-methyltransferase 1 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 qualifier: involved_in review: summary: >- PMT1 is part of a wound-inducible defense program, but this is context-level biology rather than its defining enzymatic function. action: KEEP_AS_NON_CORE reason: >- The 2001 N. attenuata study supports wound-responsive transcript induction, so the annotation should be preserved as non-core. supported_by: - reference_id: file:NICAT/NaPMT1.1/NaPMT1.1-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 qualifier: involved_in review: summary: >- This annotation is supported by herbivory-induced PMT transcript accumulation, but it is not part of the catalytic core function. action: KEEP_AS_NON_CORE reason: >- PMT1 participates in a defense response to Manduca sexta herbivory through inducible expression linked to nicotine production. supported_by: - reference_id: file:NICAT/NaPMT1.1/NaPMT1.1-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 qualifier: involved_in review: summary: >- The experimental evidence supports jasmonate-responsive expression of PMT1, but this should remain a contextual non-core annotation. action: KEEP_AS_NON_CORE 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. supported_by: - reference_id: file:NICAT/NaPMT1.1/NaPMT1.1-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: file:NICAT/NaPMT1.1/NaPMT1.1-record-evidence.yaml title: Compact archived record and sequence evidence for Q93XQ5 - 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/NaPMT1.1/NaPMT1.1-uniprot.txt title: UniProt entry Q93XQ5 for Nicotiana attenuata PMT1 findings: - statement: UniProt identifies Q93XQ5 as Putrescine N-methyltransferase 1 record_section: [DE] supporting_text: 'DE RecName: Full=Putrescine N-methyltransferase 1' reference_section_type: DATABASE_ENTRY - statement: UniProt assigns PMT1 to nicotine biosynthesis record_section: ["CC:PATHWAY"] supporting_text: 'CC -!- PATHWAY: Alkaloid biosynthesis; nicotine biosynthesis.' reference_section_type: DATABASE_ENTRY - statement: UniProt reports predominant root expression for PMT1 record_section: ["CC:TISSUE SPECIFICITY"] supporting_text: 'CC -!- TISSUE SPECIFICITY: Mainly expressed in roots.' reference_section_type: DATABASE_ENTRY - id: file:NICAT/NaPMT1.1/NaPMT1.1-notes.md title: NaPMT1.1 literature review notes findings: - statement: PMT1 is the reviewed Nicotiana attenuata PMT1 pathway enzyme supporting_text: UniProt curates Q93XQ5 as Putrescine N-methyltransferase 1 and places it in nicotine biosynthesis with predominant root expression. reference_section_type: LITERATURE_REVIEW - statement: PMT catalyzes 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 PMT1 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: PMT1 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: PMT1 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: >- PMT1 catalyzes the S-adenosylmethionine-dependent methylation of putrescine to N-methylputrescine, which commits polyamine-derived flux into the pyrrolidine branch of nicotine biosynthesis in Nicotiana attenuata roots. supported_by: - reference_id: file:NICAT/NaPMT1.1/NaPMT1.1-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/NaPMT1.1/NaPMT1.1-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 biochemically interchangeable in vivo, or do they make distinct quantitative contributions to nicotine production under herbivory? - question: Does the more weakly characterized PMT3 paralog contribute measurable catalytic flux to the nicotine pathway, or is it a noncore duplicate? suggested_experiments: - description: 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. experiment_type: genetic perturbation plus metabolite profiling hypothesis: PMT1 and PMT2 jointly provide the dominant committed methyltransferase activity for inducible nicotine biosynthesis. - description: Compare recombinant PMT1 and PMT2 kinetic parameters with putrescine and related diamines to test whether the paralogs are catalytically redundant or subtly specialized. experiment_type: biochemical enzyme assay hypothesis: The two root PMT paralogs retain the same core activity but may differ in catalytic efficiency or inducible pathway contribution.