Fusarium Protein Toolkit: AI-powered tools to combat fungal threats to agriculture

Abstract

Background: The fungal genus Fusarium poses significant threats to food security and safety worldwide because it consists of numerous species that cause destructive diseases in crops, as well as mycotoxin contamination. The adverse effects of climate change are exacerbating some existing threats and causing new problems. These challenges highlight the need for innovative solutions, including the development of advanced tools to identify targets to control crop diseases and mycotoxin contamination incited by Fusarium. Description: In response to these challenges, we developed the Fusarium Protein Toolkit (FPT, https://fusarium.maizegdb.org/), a web-based tool that allows users to interrogate the structural and variant landscape within the Fusarium pan-genome. FPT offers a comprehensive approach to understanding and mitigating the detrimental effects of Fusarium on agriculture. The tool displays both AlphaFold and ESMFold-generated protein structure models from six Fusarium species. The structures are accessible through a user-friendly web portal and facilitate comparative analysis, functional annotation inference, and identification of related protein structures. Using a protein language model, FPT predicts the impact of over 270 million coding variants in two of the most agriculturally important species, Fusarium graminearum, which causes Fusarium head blight and trichothecene mycotoxin contamination of cereals, and F. verticillioides, which causes ear rot and fumonisin mycotoxin contamination of maize. To facilitate the assessment of naturally occurring genetic variation, FPT provides variant effect scores for proteins in a Fusarium pan-genome constructed from 22 diverse species. The scores indicate potential functional consequences of amino acid substitutions and are displayed as intuitive heatmaps using the PanEffect framework. Conclusion: FPT fills a knowledge gap by providing previously unavailable tools to assess structural and missense variation in proteins produced by Fusarium, the most agriculturally important group of mycotoxin-producing plant pathogens. FPT will deepen our understanding of pathogenic mechanisms in Fusarium, and aid the identification of genetic targets that can be used to develop control strategies that reduce crop diseases and mycotoxin contamination. Such targets are vital to solving the agricultural problems incited by Fusarium, particularly evolving threats affected by climate change. By providing a novel approach to interrogate Fusarium-induced crop diseases, FPT is a crucial step toward safeguarding food security and safety worldwide.