EffectorK, a comprehensive resource to mine for Ralstonia, Xanthomonas, and other published effector interactors in the Arabidopsis proteome

Abstract

Pathogens deploy effector proteins that interact with host proteins to manipulate the host physiology to the pathogen's own benefit. However, effectors can also be recognized by host immune proteins, leading to the activation of defence responses. Effectors are thus essential components in determining the outcome of plant–pathogen interactions. Despite major efforts to decipher effector functions, our current knowledge on effector biology is scattered and often limited. In this study, we conducted two systematic large‐scale yeast two‐hybrid screenings to detect interactions between Arabidopsis thaliana proteins and effectors from two vascular bacterial pathogens: Ralstonia pseudosolanacearum and Xanthomonas campestris. We then constructed an interactomic network focused on Arabidopsis and effector proteins from a wide variety of bacterial, oomycete, fungal, and invertebrate pathogens. This network contains our experimental data and protein–protein interactions from 2,035 peer‐reviewed publications (48,200 Arabidopsis–Arabidopsis and 1,300 Arabidopsis–effector protein interactions). Our results show that effectors from different species interact with both common and specific Arabidopsis interactors, suggesting dual roles as modulators of generic and adaptive host processes. Network analyses revealed that effector interactors, particularly “effector hubs” and bacterial core effector interactors, occupy important positions for network organization, as shown by their larger number of protein interactions and centrality. These interactomic data were incorporated in EffectorK, a new graph‐oriented knowledge database that allows users to navigate the network, search for homology, or find possible paths between host and/or effector proteins. EffectorK is available at http://www.effectork.org and allows users to submit their own interactomic data.

The large, diverse, and robust arsenal of Ralstonia solanacearum type III effectors and their in planta functions

“…Some effectome-scale experiments have tried to shed light on the function of RSSC T3Es through systematic determination of their ability to induce a hypersensitive response (HR; Wroblewski et al, 2009), inhibit plant defences (Nakano and Mukaihara, 2019a), or identify their plant targets (González-Fuente et al, 2020). However, most of our current knowledge on effector function comes from smaller-scale experiments in which often one or a few T3Es are studied.…”

“…One of the main factors complicating this task is the observed genetic redundancy among different RSSC T3Es (Angot et al, 2006;Solé et al, 2012;Chen et al, 2014). This redundancy is likely to ensure a more robust virulence strategy for the bacteria (Ghosh and O'Connor, 2017), although it makes the functional dissection of single effectors more complicated, particularly for the paralog families. Nevertheless, some members of these families can still have specific and nonredundant functions (Angot et al, 2006;Turner et al, 2009;Wang et al, 2016).…”

From effectors to effectomes: Are functional studies of individual effectors enough to decipher plant pathogen infectious strategies?

“…To achieve the functional characterization of effectomes, we must take into account that effector functions are host dependent as they acquire their “functional sense” only in association with their plant cognate interactors ( Fig 2B ). Effectors tend to target multiple highly connected host proteins [ 22 , 26 , 27 , 48 , 49 ] but may also specifically interact with nucleic acids [ 50 , 51 ] or metabolites from the pathogen or the host [ 52 – 54 ]. Therefore, the function of a full effectome largely depends on the host target repertoire, or “targetome,” as well as on the interactions among its components ( Fig 1C ) as proposed [ 55 ].…”

Keeping in Touch with Type-III Secretion System Effectors: Mass Spectrometry-Based Proteomics to Study Effector–Host Protein–Protein Interactions

“…Representative studies in which Y2H-seq was applied to study EH-PPIs include the identification of interactors of the HopZ2 (Hrp-dependent outer protein Z2) T3E from P. syringae implicated in plant host colonization [39] and the large-scale Y2H-screening for mapping interactions between effectors from the plant vascular pathogens R. solanacearum and X. campestris and A. thaliana protein [40]. However, high rates of false negative and positive interactions have been reported in Y2H-screens due to the non-physiological interaction conditions [41]. Recent advances in mass spectrometry (MS)-based proteomics strategies have unlocked opportunities for high-throughput and sensitive detection of EH-PPIs.…”