Effector Identification in Plant Pathogens

Abstract

Effectors play a central role in determining the outcome of plant−pathogen interactions. As key virulence proteins, effectors are collectively indispensable for disease development. By understanding the virulence mechanisms of effectors, fundamental knowledge of microbial pathogenesis and disease resistance have been revealed. Effectors are also considered double-edged swords because some of them activate immunity in disease resistant plants after being recognized by specific immune receptors, which evolved to monitor pathogen presence or activity. Characterization of effector recognition by their cognate immune receptors and the downstream immune signaling pathways is instrumental in implementing resistance. Over the past decades, substantial research effort has focused on effector biology, especially concerning their interactions with virulence targets or immune receptors in plant cells. A foundation of this research is robust identification of the effector repertoire from a given pathogen, which depends heavily on bioinformatic prediction. In this review, we summarize methodologies that have been used for effector mining in various microbial pathogens which use different effector delivery mechanisms. We also discuss current limitations and provide perspectives on how recently developed analytic tools and technologies may facilitate effector identification and hence generation of a more complete vision of host−pathogen interactions. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

A recently collected Xanthomonas translucens isolate encodes TAL effectors distinct from older, less virulent isolates

“…Bacterial virulence and aggression are typically linked to the expression of different effector repertoires, which can increase virulence by suppressing the plant immune system, making nutrients more available to the pathogen, or changing the plant environment to better support population growth, making virulence factors indispensable for disease development [54,55]. TALEs are one example of a class of virulence effectors, which typically suppress plant resistance genes and/or activate susceptibility genes by modulating plant gene expression through plant promoters [56].…”

Beav: A bacterial genome and mobile element annotation pipeline

“…While Beav annotates genes with similarity to known secreted effectors, it currently does not identify novel effectors de novo . There are many published tools for the de novo identification of type III and type IV secreted proteins 3 . However, in our testing, none of these tools were consistent in identifying known effectors or were only available as webservers, and several tools identified many false positives that are unlikely to encode for secreted proteins.…”

“…However, annotation of many phytopathogens and plant-associated microbes often fails to identify and name key genes important for plant-microbe interactions, symbiosis, and virulence. For instance, effector proteins secreted by phytopathogens have a fundamental role in the plant disease process, yet they are underrepresented in annotation tools and databases 3 . While these key virulence loci may be characterized and classified in species-specific databases and publications, these annotations are often not incorporated into annotation databases or current tools.…”

Pseudomonas syringaepv.tomatoDC3000 induces defense responses in diverse maize inbred lines

“…To facilitate disease development, plant phytopathogens often secrete a repertoire of virulence proteins, known as effectors, to host cells during the infection process (Bentham et al, 2020). The primary function of these pathogen-secreted effectors is to manipulate host cell physiology and development, including the structure and function of plant cells as well as modulate host immune responses (Bentham et al, 2020; Lovelace et al, 2023). To circumvent the immune-suppressing activities of diverse plant phytopathogens, plants have evolved a two-tiered, integrated immune signaling network (Bentham et al, 2020; Lovelace et al, 2023; Ngou et al, 2022).…”

“…The primary function of these pathogen-secreted effectors is to manipulate host cell physiology and development, including the structure and function of plant cells as well as modulate host immune responses (Bentham et al, 2020; Lovelace et al, 2023). To circumvent the immune-suppressing activities of diverse plant phytopathogens, plants have evolved a two-tiered, integrated immune signaling network (Bentham et al, 2020; Lovelace et al, 2023; Ngou et al, 2022). The first tier, often referred to as cell surface-triggered immunity, primarily involves the detection of pathogen-associated molecular pattern (PAMPs) by cell surface-localized, transmembrane immune receptors) (Bentham et al, 2020; Ngou et al, 2022).…”