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Classification of polyphenol oxidases shows ancient gene duplication leading to two distinct enzyme types

Summary

Scientists performed a comprehensive study organizing thousands of similar enzymes called polyphenol oxidases (PPOs) found across all living organisms into 12 distinct groups based on their evolutionary relationships. They discovered that a major gene duplication event in ancient times created two main types of these enzymes with different structural features and functions. This new classification system shows that fungal enzymes called o-methoxy phenolases are particularly abundant in certain fungi, likely helping them break down plant materials like lignin.

Background

Polyphenol oxidases (PPOs) are coupled binuclear copper proteins found across all domains of life that catalyze the oxidation of phenols. These enzymes perform diverse functions including melanin biosynthesis, specialized metabolite synthesis, and lignin degradation. Recent discoveries of fungal o-methoxy phenolases active on lignin-derived compounds suggest broader functional diversity than previously understood.

Objective

To perform a comprehensive phylogenetic analysis of PPOs from diverse taxonomic origins and define distinct PPO groups based on evolutionary relationships. To investigate how PPO types relate to biochemical activity, substrate specificity, and genomic distribution across organisms.

Results

Classification revealed 12 distinct PPO groups (types a-l) with an ancient gene duplication event creating two major PPO types. Type 1 includes PPOs from chordates, molluscs, and fungal o-methoxy phenolases; Type 2 includes plant PPOs, hemocyanins, and fungal tyrosinases, most containing C-terminal shielding domains and thioether bonds. Ascomycetes contain high numbers of Type 1 PPOs including o-methoxy phenolases.

Conclusion

The phylogenetic classification system provides a framework for predicting PPO function and identifying new enzyme variants. The prevalence of o-methoxy phenolases in ascomycetes suggests their role in lignin utilization strategies. Further characterization of uncharacterized PPO types is needed to fully understand their functional roles and substrate specificities.
  • Published in:iScience,
  • Study Type:Phylogenetic Analysis,
  • Source: 10.1016/j.isci.2025.111771, PMID: 39925425
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