This article describes a bioinformatics pipeline to identify Type III Secretion System (T3SS) effector proteins, applies this approach to 105 Aeromonas genomes, and evaluates the cytotoxicity of the identified effectors through heterologous expression in yeast. The genetic determinants of pathogenicity are highly variable between strains and species. A factor commonly associated with virulent bacteria, including many Aeromonas spp., is the presence of a T3SS, which injects effector proteins into target eukaryotic cells. Numerous types of effectors have been identified and characterized to date. This study describes a novel bioinformatics pipeline to examine the genomes of Aeromonas strains isolated from environmental, mutualistic, or pathogenic contexts to identify T3SS effectors. The developed pipeline uses a two-step approach: first candidate families are selected using HMM profiles with minimal similarity scores against the Virulence Factors DataBase (VFDB), followed by strict comparisons against positive and negative control datasets, greatly reducing the number of false positives. Our approach identified a total of 21 Aeromonas T3SS likely effector groups, of which 8 represented known or characterized effectors, while the remaining 13 were not previously described in Aeromonas. We experimentally validated our in silico findings by assessing the cytotoxicity of representative effectors in Saccharomyces cerevisiae BY4741. Out of 21 assayed proteins, 17 elicited a cytotoxic effect in yeast.This study demonstrates the utility of our approach, combining a novel in silico search method with in vivo experimental validation, and will be useful in future research aimed at identifying and authenticating bacterial effector proteins from other genera. * The e-Xtra logo stands for "electronic extra" and indicates that six supplementary figures and one supplementary table are published online. e-Xtra * 7.2 Revisão sobre Ca. Liberibacter spp. Juntamente com o Prof. Setubal e o Dr. Joaquim Martins fui co-autor da revisão sobre Liberibacter spp., que será publicada na Annual Review of Phytopathology.Fomos responsáveis pelas análises de genômica comparativa envolvendo 19 genomas de Liberibacter spp. disponíveis atualmente. Dentre as análises nós classificamos os genes preditos nos 19 genomas de acordo com suas atividades em vias do KEGG, identificamos diferentes enriquecimentos de vias em diferentes genomas, e a composição do pan e coregenoma.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.