Interchromosomal Transfer of Immune Regulation During Infection of Barley with the Powdery Mildew Pathogen

Surana, Priyanka; Xu, Ruo; Fuerst, Greg; Chapman, Antony V. E.; Nettleton, Dan; Wise, Roger P.

doi:10.1534/g3.117.300125

Cited by 8 publications

(14 citation statements)

References 78 publications

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“…Additionally, as a proof of concept, we used Y2H-SCORES to identify and confirm the interaction of the barley powdery mildew effector, AVRA13, with the barley vesicle-mediated thylakoid membrane biogenesis protein, HvTHF1. This interaction, accompanied with previous evidence (21) and expression quantitative trait loci (eQTL) associations (22), support the involvement of HvTHF1 with resistance to powdery mildew.…”

Section: Introductionsupporting

confidence: 74%

“…In addition, THF1 also has been found to destabilize several NB-LRR-type resistance proteins by binding their I2-like coiled-coil (CC) domains (41). Previous eQTL analysis performed by our group, combined with an interlogs search, revealed significant associations of Thf1 and its primary interactors with the Mla1 and MlLa trans-eQTL (22). These trans-eQTL associations ( Fig 4C) were observed at different powdery mildew infection stages, MlLa at penetration, and Mla1 during haustorial development.…”

Section: Experimental Validation Of Y2h-scores Identifies a New Intermentioning

confidence: 95%

“…As illustrated inFig 4C, we found 18predicted interactions with four main protein families: Homeobox protein BEL1, DOF zinc finger protein, protein kinase, receptor kinase and leucin-rich receptor-like kinase. Interestingly, previous expression quantitative trait locus (eQTL) analysis indicated that Thf1 associates significantly with the Mla1 (mildew resistance locus a1) trans-eQTL(22). Many of the predicted interactors for the THF1 protein are also associated with trans-eQTL at different powdery mildew infection stages, MlLa (Laevigatum resistance locus) at penetration and Mla1 during haustorial development(22).…”

mentioning

confidence: 99%

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Y2H-SCORES: A statistical framework to infer protein-protein interactions from next-generation yeast-two-hybrid sequence data

Velásquez-Zapata

Elmore

Banerjee

et al. 2020

Preprint

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Interactomes embody one of the most effective representations of cellular behavior by revealing function through protein associations. In order to build these models at the organism scale, highthroughput techniques are required to identify interacting pairs of proteins. Next-generation interaction screening (NGIS) protocols that combine yeast two-hybrid (Y2H) with deep sequencing are promising approaches to generate protein-protein interaction networks in any organism. However, challenges remain to mining reliable information from these screens and thus, limit its broader implementation. Here, we describe a statistical framework, designated Y2HSCORES, for analyzing high-throughput Y2H screens that considers key aspects of experimental design, normalization, and controls. Three quantitative ranking scores were implemented to identify interacting partners, comprising: 1) significant enrichment under selection for positive interactions, 2) degree of interaction specificity among multi-bait comparisons, and 3) selection of in-frame interactors. Using simulation and an empirical dataset, we provide a quantitative assessment to predict interacting partners under a wide range of experimental scenarios, facilitating independent confirmation by one-to-one bait-prey tests. Simulation of Y2H-NGIS identified conditions that maximize detection of true interactors, which can be achieved with protocols such as prey library normalization, maintenance of larger culture volumes and replication of experimental treatments. Y2H-SCORES can be implemented in different yeastbased interaction screenings, accelerating the biological interpretation of experimental results. Proof-of-concept was demonstrated by discovery and validation of a novel interaction between the barley powdery mildew effector, AVRA13, with the vesicle-mediated thylakoid membrane biogenesis protein, HvTHF1.

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Section: Introductionsupporting

confidence: 74%

Section: Experimental Validation Of Y2h-scores Identifies a New Intermentioning

confidence: 95%

mentioning

confidence: 99%

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Y2H-SCORES: A statistical framework to infer protein-protein interactions from next-generation yeast-two-hybrid sequence data

Velásquez-Zapata

Elmore

Banerjee

et al. 2020

Preprint

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“…Different processes associated with the targets included signaling, transcriptional regulation, and intracellular trafficking. In addition, when we integrated these results with previous expression quantitative trait locus (eQTL) analysis [39], we found that several MLA6 targets and/or secondary interactors associate significantly with the Mla1 (mildew resistance locus a1) and…”

Section: Y2h-scores Discards Auto-active Preys and Identifies Novel Interactors Of The Mla6 Barley Powdery Mildew Resistance Proteinmentioning

confidence: 87%

“…Rows followed by an asterisk ( � ) designate protein MlLa (Laevigatum resistance locus) trans-eQTL. These trans-eQTL associations occur at different powdery mildew infection stages, MlLa at fungal penetration and Mla1 during haustorial development (Table B in S9 Data) [39], and may provide clues as to the temporal control of these interactors in the immune response of barley to powdery mildew.…”

Section: Fig 6 Experimental Validation Of the Interaction Between The Mla6 Nlr Receptor And Barley Targetsmentioning

confidence: 99%

Next-generation yeast-two-hybrid analysis with Y2H-SCORES identifies novel interactors of the MLA immune receptor

et al. 2021

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Protein-protein interaction networks are one of the most effective representations of cellular behavior. In order to build these models, high-throughput techniques are required. Next-generation interaction screening (NGIS) protocols that combine yeast two-hybrid (Y2H) with deep sequencing are promising approaches to generate interactome networks in any organism. However, challenges remain to mining reliable information from these screens and thus, limit its broader implementation. Here, we present a computational framework, designated Y2H-SCORES, for analyzing high-throughput Y2H screens. Y2H-SCORES considers key aspects of NGIS experimental design and important characteristics of the resulting data that distinguish it from RNA-seq expression datasets. Three quantitative ranking scores were implemented to identify interacting partners, comprising: 1) significant enrichment under selection for positive interactions, 2) degree of interaction specificity among multi-bait comparisons, and 3) selection of in-frame interactors. Using simulation and an empirical dataset, we provide a quantitative assessment to predict interacting partners under a wide range of experimental scenarios, facilitating independent confirmation by one-to-one bait-prey tests. Simulation of Y2H-NGIS enabled us to identify conditions that maximize detection of true interactors, which can be achieved with protocols such as prey library normalization, maintenance of larger culture volumes and replication of experimental treatments. Y2H-SCORES can be implemented in different yeast-based interaction screenings, with an equivalent or superior performance than existing methods. Proof-of-concept was demonstrated by discovery and validation of novel interactions between the barley nucleotide-binding leucine-rich repeat (NLR) immune receptor MLA6, and fourteen proteins, including those that function in signaling, transcriptional regulation, and intracellular trafficking.

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A Genomic View of Biotic Stress Resistance

Elmore

Perović

Ordon

et al. 2018

Compendium of Plant Genomes

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Interchromosomal Transfer of Immune Regulation During Infection of Barley with the Powdery Mildew Pathogen

Cited by 8 publications

References 78 publications

Y2H-SCORES: A statistical framework to infer protein-protein interactions from next-generation yeast-two-hybrid sequence data

Y2H-SCORES: A statistical framework to infer protein-protein interactions from next-generation yeast-two-hybrid sequence data

Next-generation yeast-two-hybrid analysis with Y2H-SCORES identifies novel interactors of the MLA immune receptor

A Genomic View of Biotic Stress Resistance

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