Molecular cloning and tissue-specific transcriptional regulation of the first peroxidase family member, Udp1, in stinging nettle (Urtica dioica)

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.

Evolution and expression of class III peroxidases

Class III peroxidases are members of a large multigenic family, only detected in the plant kingdom and absent from green algae sensu stricto (chlorophyte algae or Chlorophyta). Their evolution is thought to be related to the emergence of the land plants. However class III peroxidases are present in a lower copy number in some basal Streptophytes (Charapyceae), which predate land colonization. Gene structures are variable among organisms and within species with respect to the number of introns, but their positions are highly conserved. Their high copy number, as well as their conservation could be related to plant complexity and adaptation to increasing stresses. No specific function has been assigned to respective isoforms, but in large multigenic families, particular structure-function relations can be expected. Plant peroxidase sequences contain highly conserved residues and motifs, variable domains surrounded by conserved residues and present a low identity level among their promoter regions, further suggesting the existence of sub-functionalization of the different isoforms.

Molecular cloning and characterization of a flower-specific class III peroxidase gene in G. hirsutum

A fundamental focus of plant biology is to understand the relationship between flowering and plant reproduction, but it is also of practical interest in agriculture. To investigate the genes involved in flowering, reproduction and male sterility, DDRT-PCR was performed in vegetative and reproductive tissues of the cotton genic male sterile line LangA. A 683 bp partial peroxidase cDNA was amplified from cotton (G. hirsutum) pollen, using degenerate oligonucleotide primers and arbitrary primers in DDRT-PCR. The full-length cDNA clone, designated Ghpod (cDNA GenBank accession number: EU196676), was isolated using 5'-RACE strategy and a partial 5'-UTR was isolated applying TAIL-PCR. Ghpod was characterized as a mature 330 amino acid protein, containing all evolutionarily conserved residues present in different members of the plant peroxidase family. The molecular mass of this unprocessed and unmodified deduced protein was estimated to be 35.54 kDa, and the pI value was 4.34. According to the Ghpod protein localization prediction by PSORT, Ghpod may be secreted extracellularly. Unlike other cotton class III peroxidases, Ghpod was expressed exclusively in reproductive organs, particularly pollen. A genomic DNA fragment encoding Ghpod was also cloned and fully sequenced, revealing a "three intron" structural organization in a category of genes belonging to a normal class III plant secretory peroxidase. In conclusion, the flower-specific expression of Ghpod, predominantly in pollen, suggested that the peroxidase is involved in the male reproductive processes of angiosperms.