ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Functional and Applied Plant Genomics
This article is part of the Research TopicEvolutionary Adaptations of Plant Genes: A Comprehensive Study of Phylogenomics, Epigenetic Changes, and Protein DynamicsView all 17 articles
Gene expression and evolution of Bowman-Birk protease inhibitors (BBIs) in wild and domesticated Vigna (Fabaceae) species
Provisionally accepted
Elisa Toini1,2*
Maria Totaro1,3
Giuseppe Silvestri1
Jacopo Vertemara1Giovanni Zecca1,2
Davide Panzeri1
Emily Palm1
Robert Philipp Wagensommer3Giuseppe Zampella1
Massimo Labra1,2
Fabrizio Grassi1,2*- 1Department of Biotechnology and Bioscience, University of Milano-Bicocca, Milan, Italy
- 2NBFC, National Biodiversity Future Center, Palermo, Italy
- 3Faculty of Education, Free University of Bozen-Bolzano, Brixen-Bressanone, Italy
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Bowman-Birk protease inhibitors (BBIs) are multifunctional proteins with a double-headed structure, featuring two distinct inhibitory loops that target trypsin and chymotrypsin proteases. BBI regulates protease activity in plants and provides defense against pests and pathogens, but little is still known about their expression levels and their ability to interact with natural targets. Our results showed that BBI1 and BBI2 genes are the most highly expressed in Vigna seeds. Consequently, we produced two multiple sequence alignments including homologs from 42 Vigna taxa to explore variability and functionality. Phylogenetic relationships, signals of positive selection, and interaction energy levels with their natural targets were inferred. Overall, BBI2 exhibited the highest affinity for the assessed targets compared to BBI1. Amino acid substitutions have led to distinct protein variants across species, each displaying different interaction capacities with their respective targets. Additionally, the residue conferring inhibitory specificity for trypsin, located in the first domain, was found to be under positive selection in both genes. This suggests an ongoing evolutionary process aimed at optimizing affinity with proteases through continuous adaptation. Finally we emphasize that findings obtained can be used to drive the activity of plant breeders and more efficient cultivars can be selected. Given the growing availability of genomic information of wild and domesticated accessions, docking simulations offer a convenient and effective method to preliminarily assess new protein variants.
Keywords: binding energy, Bioprospecting, Bowman-birk protease inhibitors, Fabaceae, gene diversity, Vigna
Received: 01 Jul 2025; Accepted: 19 Dec 2025.
Copyright: © 2025 Toini, Totaro, Silvestri, Vertemara, Zecca, Panzeri, Palm, Wagensommer, Zampella, Labra and Grassi. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Elisa Toini
Fabrizio Grassi
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