2020
DOI: 10.1371/journal.ppat.1009012
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Effector prediction and characterization in the oomycete pathogen Bremia lactucae reveal host-recognized WY domain proteins that lack the canonical RXLR motif

Abstract: Pathogens that infect plants and animals use a diverse arsenal of effector proteins to suppress the host immune system and promote infection. Identification of effectors in pathogen genomes is foundational to understanding mechanisms of pathogenesis, for monitoring field pathogen populations, and for breeding disease resistance. We identified candidate effectors from the lettuce downy mildew pathogen Bremia lactucae by searching the predicted proteome for the WY domain, a structural fold found in effectors tha… Show more

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Cited by 37 publications
(39 citation statements)
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“…Training sets: Positive (effectors) and negative (non-effectors) Our positive training set consisted of oomycete effectors experimentally shown to be either recognized by R genes (avirulence activity) or to have an immune-suppressing effect on the host (virulence activity) (Supplemental Table 1). Seventy-seven of these sequences were obtained from the Pathogen-Host Interaction database (PHI-base) (Urban et al 2019) and 15 effector candidates were added from B. lactucae that had avirulence (Giesbers et al 2017;Pelgrom et al 2019;Stassen et al 2013;Wood et al 2020) or virulence activity (Wood et al 2020) resulting in an initial set of 92 sequences. We then used CD-Hit at a sequence identity threshold of 70% and word length of five amino acids in order to identify and remove closely related sequences (Fu et al 2012;Li and Godzik 2006), resulting in a final positive training set of 88 unique oomycete effectors.…”
Section: Methodsmentioning
confidence: 99%
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“…Training sets: Positive (effectors) and negative (non-effectors) Our positive training set consisted of oomycete effectors experimentally shown to be either recognized by R genes (avirulence activity) or to have an immune-suppressing effect on the host (virulence activity) (Supplemental Table 1). Seventy-seven of these sequences were obtained from the Pathogen-Host Interaction database (PHI-base) (Urban et al 2019) and 15 effector candidates were added from B. lactucae that had avirulence (Giesbers et al 2017;Pelgrom et al 2019;Stassen et al 2013;Wood et al 2020) or virulence activity (Wood et al 2020) resulting in an initial set of 92 sequences. We then used CD-Hit at a sequence identity threshold of 70% and word length of five amino acids in order to identify and remove closely related sequences (Fu et al 2012;Li and Godzik 2006), resulting in a final positive training set of 88 unique oomycete effectors.…”
Section: Methodsmentioning
confidence: 99%
“…Two distinct alleles were obtained. Agrobacterium tumefaciens strain C58Rif+ was transformed with pEG100-BLE01 and infiltrations were performed on three- to five-week-old lettuce plants as described previously (Wood et al 2020). Leaves were scored for necrosis 4-5 days after infiltration.…”
Section: Methodsmentioning
confidence: 99%
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“…Some RXLRs possess an additional motif in the C‐terminus involving repeats of the amino acids W, Y, and L (Haas et al, 2009; Jiang et al, 2008). Recent reports emphasize the importance of WY domain‐containing effectors that lack a canonical RXLR motif in downy mildew pathogens (Derevnina et al, 2015; Wood et al, 2020). In line with this, there were 74 such effectors in the secretome of P .…”
Section: Genome Resources and Virulence Factorsmentioning
confidence: 99%
“…Furthermore, the RxLR motif is not conserved outside Phytophthora species and downy mildews. The WY domain is a structural domain associated with cytoplasmic oomycete effectors from the Peronosporales that has been used to identify effector candidates with degenerate RxLR motifs (Wood et al , 2020). Similarly, degenerate RxLR motif searches have been applied in Pythium species that lack effectors with a canonical RxLR motif (Ai et al , 2020).…”
Section: Introductionmentioning
confidence: 99%