Biology subjects

Homma, F.

Publications and source records attributed to Homma, F..

3 recordsLinked to original sources

bioRxiv2024

Using AlphaFold Multimer to discover interkingdom protein-protein interactions

Structural prediction by artificial intelligence (AI) can be powerful new instruments to discover novel protein-protein interactions, but the community still grapples with the implementation, opportunities and limitations. Here, we discuss and re-analyse our in-silico screen for novel pathogen-secreted inhibitors of immune hydrolases to illustrate the power and limitations of structural predictions. We discuss strategies of curating sequences, including controls, and reusing sequence alignments and highlight important limitations originating from platforms, sequence depth and computing times. We hope these experiences will support similar interactomic screens by the research community.

plant biology↗

bioRxiv2023

Alphafold-multimer predicts cross-kingdom interactions at the plant-pathogen interface

Adapted plant pathogens from various microbial kingdoms produce hundreds of unrelated small secreted proteins (SSPs) with elusive roles. Some of these SSPs might be inhibitors targeting the most harmful hydrolases secreted by the host. Here, we used Alphafold-Multimer (AFM) to screen 1,879 SSPs of seven tomato pathogens for interacting with six defence-related hydrolases of tomato that accumulate to high levels in the apoplast during infection. This screen of 11,274 protein pairs identified 15 SSPs that are predicted to obstruct the active site of chitinases and proteases with an intrinsic fold. Four SSPs were experimentally verified to be inhibitors of pathogenesis-related subtilase P69B, including extracellular protein-36 (Ecp36) and secreted-into-xylem-15 (Six15) of the fungal tomato pathogens Cladosporium fulvum and Fusarium oxysporum, respectively. Together with a novel P69B inhibitor from the bacterial pathogen Xanthomonas perforans and the previously reported Kazal-like inhibitors of the oomycete pathogen Phytophthora infestans, P69B emerges as an important effector hub targeted by different microbial kingdoms, consistent with the presence of a hyper-variant residue in P69B orthologs and gene duplication and diversification of P69B paralogs that could avoid inhibitor binding. This study demonstrates the power of artificial intelligence to accurately predict novel cross-kingdom interactions at the plant-pathogen interface.

plant biology↗

bioRxiv2018

Re-annotated Nicotiana benthamiana gene models for enhanced proteomics and reverse genetics

Nicotiana benthamiana is an important model organism and representative of the Solanaceae (Nightshade) family. N. benthamiana has a complex ancient allopolyploid genome with 19 chromosomes, and an estimated genome size of 3.1Gb. Several draft assemblies of the N. benthamiana genome have been generated, however, many of the gene-models in these draft assemblies appear incorrect. Here we present a nearly non-redundant database of 42,855 improved N. benthamiana gene-models. With an estimated 97.6% completeness, the new predicted proteome is more complete than the previous proteomes. We show that the database is more sensitive and accurate in proteomics applications, while maintaining a reasonable low gene number. As a proof-of-concept we use this proteome to compare the leaf extracellular (apoplastic) proteome to a total extract of leaves. Several gene families are more abundant in the apoplast. For one of these apoplastic protein families, the subtilases, we present a phylogenetic analysis illustrating the utility of this database. Besides proteome annotation, this database will aid the research community with improved target gene selection for genome editing and off-target prediction for gene silencing.

plant biology↗