Fungal Effectoromics: A World in Constant Evolution

Abstract

Effectors are small, secreted molecules that mediate the establishment of interactions in nature. While some concepts of effector biology have stood the test of time, this area of study is ever-evolving as new effectors and associated characteristics are being revealed. In the present review, the different characteristics that underly effector classifications are discussed, contrasting past and present knowledge regarding these molecules to foster a more comprehensive understanding of effectors for the reader. Research gaps in effector identification and perspectives for effector application in plant disease management are also presented, with a focus on fungal effectors in the plant-microbe interaction and interactions beyond the plant host. In summary, the review provides an amenable yet thorough introduction to fungal effector biology, presenting noteworthy examples of effectors and effector studies that have shaped our present understanding of the field.

In Silico Characterization of the Secretome of the Fungal Pathogen Thielaviopsis punctulata, the Causal Agent of Date Palm Black Scorch Disease

“…EffectorP, combined with the manual inspection, was employed to identify the putative effector proteins with the following characteristics: a signal peptide for secretion, no trans-membrane domains, fairly small size, and cysteine-rich [ 9 , 31 , 60 ]. This analysis resulted in the identification of 47 proteins as putative “effector” candidates ( Figure 6 ).…”

“…This layer of immunity is called PAMP-triggered immunity (PTI) [ 5 ]. Although PTI is effective against a broad spectrum of microorganisms, pathogens overcome PTI by secreting so-called effector proteins that manipulate cellular processes in the host to facilitate effector-triggered susceptibility (ETS) [ 6 , 7 , 8 , 9 , 10 ]. In turn, plants have evolved a second layer of immunity in which they employ another type of receptor called resistance (R) proteins [ 11 ].…”

AMAPEC: accurate antimicrobial activity prediction for fungal effector proteins

“…Like other non-model organisms, fungal genomes comprise a large proportion of genes that lack functional annotation, which complicates biological interpretations of genomic and transcriptomic analyses. Fungal secretomes are particularly poorly annotated by similarity-based methods (Fig 2), since they include significant numbers of fast-evolving effectors that represent recent innovations and show little conservation across the fungal kingdom 44,57 . Recently, major efforts were made to develop new functional annotation methods, relying mostly on machine-learning prediction, but these were not aimed to discover antimicrobial activities 58–62 .…”

“…However, these are inappropriate to annotate fungal effector proteins as they were trained on AMP databases 41–43 and are therefore essentially dedicated to short peptides of sizes up to 100 amino acids in length. With sequence lengths up to 850 amino acids 44 , fungal effectors are considerably larger and thus require a dedicated predictor based on a training dataset that incorporates larger antimicrobial proteins that likely have different properties and mode-of-actions than AMPs. Here, we describe the development of such tool and introduce the software AMAPEC (for a nti m icrobial a ctivity p rediction for e ffector c andidates), a tool to annotate candidate antimicrobial effector proteins relying on their sequence and predicted structure properties.…”

Avaliação da expressão de genes do fungo >i<Sporisorium scitamineum>/i< durante a interação com plantas de cana-energia com diferentes níveis de resistência ao carvão

“…Para S. scitamineum, temos um foco especial na identificação de efetores através de estudos comparativos entre os genomas dos fungos causadores de carvão . A caracterização de efetores se mostra complexa, posto que tais moléculas apresentam uma evolução rápida, associada a uma alta especificidade entre patógenos e hospedeiros (SPERSCHNEIDER et al, 2015;NICOLE et al, 2022). Na produção de mutantes (etapa característica do processo de validação de uma molécula efetora), as deleções únicas frequentemente não produzem um fenótipo detectável (BASSE; KOLB; KAHMANN, 2002).…”