Proteomics of Pteridium aquilinum provides insights on stem lignification mechanisms

BACKGROUND AND AIMS: Stem lignification seriously reduces the edible quality and marketability of Pteridium aquilinum, a popular wild vegetable. This study aimed to explore the molecular mechanism underlying stem lignification during longitudinal development. METHODS: We performed 4D-proteomics based on data-independent acquisition (DIA) to compare protein expression profiles in the basal, middle, and upper parts of vegetative stems. KEY RESULTS: A total of 6014 proteins were detected across basal, middle, and upper stem parts, with 1107, 647, and 234 differentially expressed proteins (DEPs) identified in basal vs upper, middle vs upper, and basal vs middle comparisons, respectively. Among 72 DEPs shared by the three groups, 17 DEPs exhibited consistent up- or down-regulation patterns along the longitudinal sections, with fold changes ranging from 2.10 to 752.36 across comparisons, and most showing strong positive correlations (r > 0.94) with lignin content. Functional classification indicated that these DEPs were mainly associated with five categories, including photosynthesis, phenylpropanoid metabolism, cell wall organization, stress response, and shikimate metabolism. Lignin content increased basipetally. In contrast, activities of POD, PAL, and 4-CL showed an acropetal pattern (lower in basal part, higher in upper part), while laccase (LAC) activity increased basipetally, consistent with the lignin gradient. DEPs related with photosynthesis and shikimate metabolism were up-regulated, which might supply potential precursors for phenylpropanoid metabolism. Key enzymes such as 4-coumarate-CoA ligase (fold change up to 454.78 in basal vs upper comparison), cinnamoyl-coA reductase (up to 34.15), and caffeyol-CoA O-methyltransferase (up to 11.81), were identified, which could potentially participate in lignin monomer biosynthesis and polymerization. CONCLUSIONS: Multiple biological processes coordinately regulate stem lignification in P. aquilinum. These results may serve as a scientific reference for future studies aiming to develop approaches to alleviate stem lignification and improve edible quality of P. aquilinum.