Cytoplasmic phenylalanine ammonia-lyase (EC 4.3.1.24) catalyzing the first committed, non-oxidative deamination of L-phenylalanine to trans-cinnamate, the entry-point reaction of the phenylpropanoid pathway. Downstream phenylpropanoid metabolism in Populus supplies monolignols/lignin in lignifying xylem and condensed tannins/flavonoids/phenolic glycosides in specialized non-lignifying tissues, with the five-member PtrPAL gene family functionally partitioned between these outputs.
The preferred accession for this review is P45730. These relationships are manually assessed.
REFERENCE PROTEOME EQUIVALENT · Reviewed 2026-10-19
Reference proteome: UP000006729
Retain P45730 as the primary Swiss-Prot accession. A0A2K1XD28 at POPTR_016G091100 is the manually assessed reference-proteome counterpart: 714/715 identical residues with full ungapped coverage and only R22L. The next full-length family match, A0A2K2A1A8 at POPTR_006G126800, has 32 substitutions and one gap column. The source sequence is from a P. trichocarpa x P. deltoides hybrid; the counterpart assignment is inferred from the sequence comparison and does not establish the parental origin or cause of R22L.
MMseqs2 searched all 77,340 sequences in UP000006729 (release 2026_03); global BLOSUM62 alignments were computed for every returned hit. A0A2K1XD28 ranks first by global alignment score, with 99.8601% identity including gap columns, 100.0% query coverage and 100.0% target coverage. The saved candidate table and alignments retain competing matches and residue-level differences. The search is heuristic, and sequence similarity alone is not definitive genomic mapping. Identity over paired residues is 99.8601% (714/715); gap columns are excluded from this denominator.
file:POPTR/PAL/PAL-record-evidence.yaml
query_length: 715 target_length: 715 alignment_columns: 715 identities: 714 mismatches: 1 gap_columns: 0 identity_percent: 99.8601 query_coverage_percent: 100.0 target_coverage_percent: 100.0
Current UniProtKB and proteome records place A0A2K1XD28, but not P45730, in reference proteome UP000006729. Both UniProt records use NCBITaxon:3694; source-organism qualifications are recorded separately.
file:POPTR/PAL/PAL-record-evidence.yaml
reference_proteome: UP000006729 proteome_is_reference: true proteome_taxon_matches: true primary_in_reference_proteome: false alternative_in_reference_proteome: true
UniSave versions 97 (2015), 113 (2020), and 124 (2024) lack Proteomes cross-references. These dated samples support longstanding absence at those dates; they do not establish uninterrupted absence, a removal event, or UniProt's motivation.
file:POPTR/PAL/PAL-record-evidence.yaml
sampled_history_versions: - 97 - 113 - 124 sampled_versions_with_proteome_links: []
Both the Swiss-Prot source citation and ENA L11747 identify a P. trichocarpa x P. deltoides hybrid. The reference proteome is Nisqually. Hybrid provenance makes a small sequence difference plausible but does not itself establish locus identity.
file:POPTR/PAL/PAL-record-evidence.yaml
/organism="Populus trichocarpa x Populus deltoides"
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003824 catalytic activity | IEA GO_REF:0000002 | MODIFY | Summary: Generic catalytic activity is correct but uninformative for a characterized PAL enzyme. Reason: Replace the root catalytic activity term with the specific phenylalanine ammonia-lyase activity term, which captures the actual reaction (L-phenylalanine to trans-cinnamate + NH4+). Proposed replacements: phenylalanine ammonia-lyase activity Supporting Evidence: file:POPTR/PAL/PAL-uniprot.txt L-phenylalanine = (E)-cinnamate + NH4(+) file:POPTR/PAL/PAL-deep-research-falcon.md non-oxidative deamination** of **L-phenylalanine** to yield **trans-cinnamic acid** |
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | ACCEPT | Summary: Cytoplasm is the reviewed UniProt location for Populus PAL. Reason: UniProt assigns PAL to the cytoplasm. Falcon notes that the retrieved Populus literature did not independently resolve a subcellular compartment for P45730, so the UniProt cytoplasmic assignment is retained as the best-supported localization. Supporting Evidence: file:POPTR/PAL/PAL-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm |
| GO:0006559 L-phenylalanine catabolic process | IEA GO_REF:0000002 | ACCEPT | Summary: L-phenylalanine catabolic process correctly captures the PAL deamination reaction. Reason: PAL deaminates L-phenylalanine to trans-cinnamate and ammonium, which is consumption (catabolism) of L-phenylalanine. Supported by the UniProt reaction and the falcon synthesis. Supporting Evidence: file:POPTR/PAL/PAL-uniprot.txt L-phenylalanine = (E)-cinnamate + NH4(+) file:POPTR/PAL/PAL-deep-research-falcon.md non-oxidative deamination** of **L-phenylalanine** to yield **trans-cinnamic acid** |
| GO:0009611 response to wounding | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: Response to wounding is a plausible downstream/defense context for phenylpropanoid metabolism but is not the core enzymatic function of PAL, and the falcon corpus provides no direct wound-response evidence for Populus PAL. Reason: Retain as non-core. The defense-related role of PAL-derived phenylpropanoids (condensed tannins, phenolic glycosides) is well supported at the pathway level, but a specific wound-response function for this protein is an ARBA electronic inference and is downstream of the committed catalytic step. Supporting Evidence: file:POPTR/PAL/PAL-deep-research-falcon.md including **lignin**, **flavonoids**, **condensed tannins (proanthocyanidins)**, and **phenolic glycosides** |
| GO:0016841 ammonia-lyase activity | IEA GO_REF:0000002 | MODIFY | Summary: Ammonia-lyase activity is correct but less specific than phenylalanine ammonia-lyase activity. Reason: Replace the grouping term with the substrate-specific phenylalanine ammonia-lyase activity term, consistent with the UniProt reaction and the falcon entry-reaction description. Proposed replacements: phenylalanine ammonia-lyase activity Supporting Evidence: file:POPTR/PAL/PAL-uniprot.txt L-phenylalanine = (E)-cinnamate + NH4(+) file:POPTR/PAL/PAL-deep-research-falcon.md non-oxidative deamination** of **L-phenylalanine** to yield **trans-cinnamic acid** |
| GO:0045548 phenylalanine ammonia-lyase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Phenylalanine ammonia-lyase activity is the core molecular function of PAL. Reason: The reaction converts L-phenylalanine to trans-cinnamate and ammonium (EC 4.3.1.24), the committed entry reaction of phenylpropanoid biosynthesis. Supporting Evidence: file:POPTR/PAL/PAL-uniprot.txt L-phenylalanine = (E)-cinnamate + NH4(+) file:POPTR/PAL/PAL-deep-research-falcon.md the canonical **entry reaction** from aromatic amino-acid metabolism into **phenylpropanoid biosynthesis** |
| GO:0046395 carboxylic acid catabolic process | IEA GO_REF:0000117 | MODIFY | Summary: Carboxylic acid catabolic process is too broad for the PAL reaction. Reason: The substrate-specific L-phenylalanine catabolic process (already accepted) is the appropriate term; the generic carboxylic acid catabolic grouping adds no information. Proposed replacements: L-phenylalanine catabolic process Supporting Evidence: file:POPTR/PAL/PAL-uniprot.txt L-phenylalanine = (E)-cinnamate + NH4(+) file:POPTR/PAL/PAL-deep-research-falcon.md non-oxidative deamination** of **L-phenylalanine** to yield **trans-cinnamic acid** |
| GO:0009800 cinnamic acid biosynthetic process | IEA GO_REF:0000041 | ACCEPT | Summary: Cinnamic acid biosynthetic process is the direct product process of PAL. Reason: PAL produces trans-cinnamate from L-phenylalanine (UniPathway step 1/1), the committed entry into phenylpropanoid metabolism. Supported by the UniProt pathway statement and the falcon entry-reaction synthesis. Supporting Evidence: file:POPTR/PAL/PAL-uniprot.txt trans-cinnamate biosynthesis file:POPTR/PAL/PAL-deep-research-falcon.md the canonical **entry reaction** from aromatic amino-acid metabolism into **phenylpropanoid biosynthesis** |
| GO:0045548 phenylalanine ammonia-lyase activity | ISS GO_REF:0000024 | ACCEPT | Summary: Phenylalanine ammonia-lyase activity transferred by sequence similarity from the experimentally characterized ortholog (UniProtKB:P24481). Reason: The ISS transfer is well founded; PAL is a conserved member of the PAL/histidase family with the autocatalytic MIO active site, and the reaction is the same committed deamination of L-phenylalanine to trans-cinnamate. |
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Download this section (compressed HTML)Q: Which Populus tissues and stresses induce this PAL isoform relative to the other four PtrPAL paralogs (PtrPAL1-PtrPAL5)?
Q: Does this PAL isoform preferentially support lignin (xylem/monolignol flux) versus condensed-tannin/flavonoid phenylpropanoid output?
Experiment: Measure phenylalanine-to-cinnamate conversion and downstream phenylpropanoid metabolite pools (monolignols, flavonoids, condensed tannins) after PAL knockdown or overexpression in Populus.
Type: targeted functional assay
Experiment: Map this PAL isoform to a specific Potri locus and resolve its subcellular localization (cytosol vs microsomal/ER association) by fractionation and fluorescent-protein fusion, since the retrieved literature did not resolve the compartment for P45730.
Type: localization and isoform-mapping study
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Download this section (compressed HTML)PAL-uniprot.txt and PAL-goa.tsv.Loading supporting content…
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