| Evidence type | Key finding | Quantitative details (with units) | Source (first author year journal) | URL | Citation ID |
|---|---|---|---|---|---|
| Gene ID mapping | Bradi3g48840 (LOC100829928) is explicitly listed as one of eight Brachypodium PAL-family genes and mapped to **BdPAL5**; all eight carry the conserved Ala-Ser-Gly triad required for the MIO catalytic group. | 8 PAL-family genes in *B. distachyon*; Bradi3g48840 transcripts were low/undetected in sampled tissues. | Cass 2015 *Journal of Experimental Botany* | https://doi.org/10.1093/jxb/erv269 | (pqac-00000007) |
| Enzyme function | Plant PAL is the entry enzyme of phenylpropanoid metabolism, catalyzing deamination of L-phenylalanine to trans-cinnamate; in grasses, related PTAL enzymes can also deaminate L-tyrosine to p-coumarate. | Reaction products measured as trans-cinnamic acid from L-Phe; in culm extracts PAL activity was ~25-fold higher than TAL activity. | Cass 2015 *Journal of Experimental Botany* | https://doi.org/10.1093/jxb/erv269 | (pqac-00000000, pqac-00000002, pqac-00000033) |
| Expression/regulation | Bradi3g48840 is hormone responsive and behaves as a JA marker gene in *Brachypodium*. | JA induction classified as **++** (>10-fold vs mock) within 24–48 h; markedly induced at 24 h and further increased at 48 h; not induced by SA or ET in the summary table. | Kouzai 2016 *BMC Plant Biology* | https://doi.org/10.1186/s12870-016-0749-9 | (pqac-00000018, pqac-00000019) |
| Localization/pathway organization | Direct localization for BdPAL5 is not reported in the retrieved gene-specific papers, but Brachypodium PTAL activity is mainly cytosolic with minor plastid/microsomal presence, and recent proximity-labeling work supports phenylpropanoid pathway organization on the cytosolic face of the ER around C4H. | Native BdPTAL1 is a tetramer of ~290 kDa with ~77 kDa subunits; Petunia C4H-TurboID identified 185 enriched proteins at 0 h and 69 at 3 h biotin labeling. | Barros 2016 *Nature Plants*; Aravena-Calvo 2024 *Frontiers in Plant Science* | https://doi.org/10.1038/nplants.2016.50 ; https://doi.org/10.3389/fpls.2024.1295750 | (pqac-00000011, pqac-00000023, pqac-00000024) |
| Phenotypes/traits | PAL knockdown in *Brachypodium* reduces lignification, alters wall phenolics, increases digestibility, and compromises some pathogen resistance, showing PAL-family genes are central to cell-wall phenylpropanoid flux. | Acid-insoluble lignin reduced by 49% and 37% in two RNAi lines; total lignin reduced by 43% and 30%; FA release reduced by 57%; glucose release increased by 93% and pentose release by 96% after alkali pretreatment + hydrolysis. | Cass 2015 *Journal of Experimental Botany* | https://doi.org/10.1093/jxb/erv269 | (pqac-00000001, pqac-00000003, pqac-00000004) |
| Quantitative data | Grass PAL/PTAL studies provide benchmark kinetic and flux values that contextualize PAL-family function in *Brachypodium*; one PTAL can contribute major lignin flux from Tyr. | BdPTAL1: Km(L-Phe) ≈ 201.2 µM, kcat ≈ 0.56 s^-1, kcat/Km ≈ 2.8 s^-1 mM^-1; Km(L-Tyr) ≈ 11.9 µM, kcat ≈ 0.07 s^-1, kcat/Km ≈ 5.9 s^-1 mM^-1; Tyr-derived route can supply nearly half of total lignin. | Barros 2016 *Nature Plants*; Yokoyama 2024 *Philosophical Transactions B* | https://doi.org/10.1038/nplants.2016.50 ; https://doi.org/10.1098/rstb.2023.0352 | (pqac-00000030, pqac-00000008, pqac-00000009) |


*Table: This table summarizes the strongest literature-backed evidence supporting annotation of LOC100829928 / Bradi3g48840 as a PAL-family enzyme in Brachypodium. It combines locus mapping, functional biochemistry, regulation, pathway context, and phenotype data relevant to annotation.*