Orthology-based analysis helps map evolutionary diversification and predict substrate class use of BAHD...

Area of Science:

• Biochemistry
• Evolutionary Biology
• Plant Science

Background:

• Enzyme families drive metabolic diversity but their functional evolution is unclear.
• Gene duplication and promiscuity in enzyme families complicate functional prediction and genome annotation.
• BAHD acyltransferases, a large plant enzyme family, exemplify these challenges with rapid expansion and diverse activities.

Purpose of the Study:

• To investigate the evolutionary mechanisms behind the functional diversity of BAHD acyltransferases.
• To develop a predictive method for BAHD acceptor substrate classes and their evolutionary origins.
• To improve the functional annotation of plant enzyme families, using BAHDs as a model.

Main Methods:

• Compiled >160 published BAHD enzyme activities to map chemical space and define substrate classes.
• Utilized orthologous groups (OGs) across 52 plant genomes to predict BAHD substrate class and evolutionary history.
• Validated the predictive method with novel and known BAHD enzymes, including molecular simulations and mutagenesis.

Main Results:

• Defined eight BAHD acceptor substrate classes based on structural similarities.
• Developed an OG-based method to predict BAHD substrate utilization and evolutionary origins.
• Showcased ancient origins for cuticular wax and lignin activities, and later acquisition of anthocyanin acylation.
• Identified signature motifs in anthocyanin-acylating BAHDs, confirming their functional importance.

Conclusions:

• BAHD acyltransferases significantly contributed to the evolution of diverse plant chemical phenotypes.
• The developed OG-based approach enhances functional annotation of plant enzyme families.
• This study provides a framework for understanding enzyme family evolution and improving genomic data.