Identification and characterization of specific motifs in effector proteins of plant parasites using MOnSTER.

Autor: Calia G; Free University of Bolzano, Faculty of Agricultural Environmental and Food Science, Bolzano, Italy.; Fondazione Edmund Mach, Research and Innovation Centre, San Michele all'Adige, Italy.; INRAE, Université Côte d'Azur, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France., Porracciolo P; INRAE, Université Côte d'Azur, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France.; Université Côte d'Azur, Center of Modeling, Simulation and Interactions, Nice, France., Chen Y; INRAE, Université Côte d'Azur, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France.; Department of Plant Pathology, China Agricultural University, Beijing, China., Kozlowski D; INRAE, Université Côte d'Azur, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France.; Université Côte d'Azur, Center of Modeling, Simulation and Interactions, Nice, France., Schuler H; Free University of Bolzano, Faculty of Agricultural Environmental and Food Science, Bolzano, Italy.; Free University of Bolzano, Competence Centre for Plant Health, Bolzano, Italy., Cestaro A; Fondazione Edmund Mach, Research and Innovation Centre, San Michele all'Adige, Italy.; Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council (CNR), Bari, Italy., Quentin M; INRAE, Université Côte d'Azur, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France., Favery B; INRAE, Université Côte d'Azur, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France., Danchin EGJ; INRAE, Université Côte d'Azur, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France., Bottini S; INRAE, Université Côte d'Azur, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France. silvia.bottini@inrae.fr.; Université Côte d'Azur, Center of Modeling, Simulation and Interactions, Nice, France. silvia.bottini@inrae.fr.
Jazyk: angličtina
Zdroj: Communications biology [Commun Biol] 2024 Jul 12; Vol. 7 (1), pp. 850. Date of Electronic Publication: 2024 Jul 12.
DOI: 10.1038/s42003-024-06515-9
Abstrakt: Plant pathogens cause billions of dollars of crop loss every year and are a major threat to global food security. Identifying and characterizing pathogens effectors is crucial towards their improved control. Because of their poor sequence conservation, effector identification is challenging, and current methods generate too many candidates without indication for prioritizing experimental studies. In most phyla, effectors contain specific sequence motifs which influence their localization and targets in the plant. Therefore, there is an urgent need to develop bioinformatics tools tailored for pathogen effectors. To circumvent these limitations, we have developed MOnSTER a specific tool that identifies clusters of motifs of protein sequences (CLUMPs). MOnSTER can be fed with motifs identified by de novo tools or from databases such as Pfam and InterProScan. The advantage of MOnSTER is the reduction of motif redundancy by clustering them and associating a score. This score encompasses the physicochemical properties of AAs and the motif occurrences. We built up our method to identify discriminant CLUMPs in oomycetes effectors. Consequently, we applied MOnSTER on plant parasitic nematodes and identified six CLUMPs in about 60% of the known nematode candidate parasitism proteins. Furthermore, we found co-occurrences of CLUMPs with protein domains important for invasion and pathogenicity. The potentiality of this tool goes beyond the effector characterization and can be used to easily cluster motifs and calculate the CLUMP-score on any set of protein sequences.
(© 2024. The Author(s).)
Databáze: MEDLINE
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