Predicting Type III Effector Proteins Using the Effectidor Web Server

Wagner, Naama; Teper, Doron; Pupko, Tal

doi:10.1007/978-1-0716-1971-1_3

Cited by 3 publications

(2 citation statements)

References 22 publications

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“…Different strategies have been used to classify effectors in other microbial kingdoms. In bacteria, effectors are classified according to the secretion system (type III, type IV) through which they are exported or translocated from the pathogen cell to the host [29,30]. In fungi, effectors that meet certain structural criteria such as small size, high cysteine content, presence of a signal peptide (SP) and absence of transmembrane domains (TMDs) are termed canonical or classical effectors, while those that do not meet some of these criteria are termed noncanonical [31][32][33]; this classification has helped to expand the size of fungal effectoromes, since the noncanonical effectors that were previously discarded contribute significantly to the overall effectorome [32].…”

Section: Introductionmentioning

confidence: 99%

Novel Insights into Phytoplasma Effectors

Carreón-Anguiano,

Vila-Luna,

Sáenz-Carbonell

et al. 2023

Horticulturae

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Effectoromics has become integral to the identification of pathogen targets and/or host-resistant proteins for the genetic improvement of plants in agriculture and horticulture. Phytoplasmas are the causal agents of more than 100 plant diseases in economically important crops such as vegetables, spices, medicinal plants, ornamentals, palms, fruit trees, etc. To date, around 20 effectors in phytoplasmas have been experimentally validated but the list of putative effectors comprises hundreds of different proteins. Very few families (tribes) have been identified based on homology, such as the SAP05-like, SAP11-like, SAP54-like and TENGU-like families. The lack of conservation in amino acid sequences slows the progress of effectoromics in phytoplasmas since many effectors must be studied individually. Here, 717 phytoplasma effector candidates and 21 validated effectors were characterized in silico to identify common features. We identified functional domains in 153 effectors, while 585 had no known domains. The most frequently identified domain was the sequence-variable mosaic domain (SVM domain), widely distributed in 87 phytoplasma effectors. Searching for de novo amino acid motifs, 50 were found in the phytoplasma effector dataset; 696 amino acid sequences of effectors had at least 1 motif while 42 had no motif at all. These data allowed us to organize effectors into 15 tribes, uncovering, for the first time, evolutionary relationships largely masked by lack of sequence conservation among effectors. We also identified 42 eukaryotic linear motifs (ELMs) in phytoplasma effector sequences. Since the motifs are related to common functions, this novel organization of phytoplasma effectors may help further advance effectoromics research to combat phytoplasma infection in agriculture and horticulture.

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Section: Introductionmentioning

confidence: 99%

Novel Insights into Phytoplasma Effectors

Carreón-Anguiano,

Vila-Luna,

Sáenz-Carbonell

et al. 2023

Horticulturae

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“…We first sequenced the genome of an Israeli isolate of Xhp, combining short and long reads to obtain high quality genome sequence. Next, we applied Effectidor (Wagner et al, 2022a;Wagner et al, 2022b;Wagner et al, 2022c) to predict T3Es in these two genomes. Our results suggested the existence of unknown T3Es in both genomes, i.e., putative T3Es without significant sequence similarity to previously identified effectors.…”

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confidence: 99%

Complete genome sequence of an Israeli isolate of Xanthomonas hortorum pv. pelargonii strain 305 and novel type III effectors identified in Xanthomonas

et al. 2023

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Xanthomonas hortorum pv. pelargonii is the causative agent of bacterial blight in geranium ornamental plants, the most threatening bacterial disease of this plant worldwide. Xanthomonas fragariae is the causative agent of angular leaf spot in strawberries, where it poses a significant threat to the strawberry industry. Both pathogens rely on the type III secretion system and the translocation of effector proteins into the plant cells for their pathogenicity. Effectidor is a freely available web server we have previously developed for the prediction of type III effectors in bacterial genomes. Following a complete genome sequencing and assembly of an Israeli isolate of Xanthomonas hortorum pv. pelargonii - strain 305, we used Effectidor to predict effector encoding genes both in this newly sequenced genome, and in X. fragariae strain Fap21, and validated its predictions experimentally. Four and two genes in X. hortorum and X. fragariae, respectively, contained an active translocation signal that allowed the translocation of the reporter AvrBs2 that induced the hypersensitive response in pepper leaves, and are thus considered validated novel effectors. These newly validated effectors are XopBB, XopBC, XopBD, XopBE, XopBF, and XopBG.

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