ROS Consumers or Producers? Interpreting Transcriptomic Data by AlphaFold Modeling Provides Insights into Class III Peroxidase Functions in Response to Biotic and Abiotic Stresses

Participating in both biotic and abiotic stress responses, plant-specific class III peroxidases (PERs) show promise as candidates for crop improvement. The multigenic PER family is known to take part in diverse functions, such as lignin formation and defense against pathogens. Traditionally linked to hydrogen peroxide (H2O2) consumption, PERs can also produce reactive oxygen species (ROS), essential in tissue development, pathogen defense and stress signaling. The amino acid sequences of both orthologues and paralogues of PERs are highly conserved, but discovering correlations between sequence differences and their functional diversity has proven difficult. By combining meta-analysis of transcriptomic data and sequence alignments, we discovered a correlation between three key amino acid positions and gene expression in response to biotic and abiotic stresses. Phylogenetic analysis revealed evolutionary pressure on these amino acids toward stress responsiveness. Using AlphaFold modeling, we found unique interdomain and protein-heme interactions involving those key amino acids in stress-induced PERs. Plausibly, these structural interactions may act as gate keepers by preventing larger substrates from accessing the heme and thereby shifting PER function from consumption to the production of ROS.

Automated summary

Plant-specific class III peroxidases (PERs) participate in both biotic and abiotic stress responses and have potential for crop improvement. The multigenic PER family is involved in various functions, including lignin formation and pathogen defense. PERs, traditionally associated with hydrogen peroxide consumption, can also produce reactive oxygen species (ROS), essential for tissue development and stress signaling. Through transcriptomic analysis and sequence alignments, we found a correlation between three key amino acid positions and gene expression in response to stresses. Phylogenetic analysis revealed evolutionary pressure on these amino acids toward stress responsiveness. AlphaFold modeling showed unique interdomain and protein-heme interactions involving those key amino acids in stress-induced PERs, suggesting their role in shifting PER function from consumption to ROS production.