In silico prediction method for plant Nucleotide‐binding leucine‐rich repeat‐ and pathogen effector interactions

The Plant Journal, Journal Year: 2025, Volume and Issue: 122(2)

Published: April 1, 2025

SUMMARY Plant Nucleotide‐binding leucine‐rich repeat (NLR) proteins play a crucial role in effector recognition and activation of Effector triggered immunity following pathogen infection. Genome sequencing advancements have led to the identification myriad NLRs numerous agriculturally important plant species. However, deciphering which recognize specific effectors remains challenging. Predicting NLR–effector interactions silico will provide more targeted approach for experimental validation, critical elucidating function, advancing our understanding NLR‐triggered immunity. In this study, protein complex structures were predicted using AlphaFold2‐Multimer all experimentally validated reported literature. Binding affinities‐ energies 97 machine learning models from Area‐Affinity. We show that acceptable accuracy can be used investigate . affinities 58 complexes ranged between −8.5 −10.6 log(K), binding −11.8 −14.4 kcal/mol −1 , depending on Area‐Affinity model used. For 2427 “forced” complexes, these estimates showed larger variability, enabling novel with 99% an Ensemble model. The narrow range energies‐ “true” suggest change Gibbs free energy, thus conformational change, is required NLR activation. This first study method predicting interactions, applicable pathosystems. Finally, NLR–Effector Interaction Classification (NEIC) resource streamline research efforts by identifying plant–pathogen resistance,

Language: Английский

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Conifers Concentrate Large Numbers of NLR Immune Receptor Genes on One Chromosome

Genome Biology and Evolution, Journal Year: 2024, Volume and Issue: 16(6)

Published: May 24, 2024

Abstract Nucleotide-binding domain and leucine-rich repeat (NLR) immune receptor genes form a major line of defense in plants, acting both pathogen recognition resistance machinery activation. NLRs are reported to large gene clusters limber pine (Pinus flexilis), but it is unknown how widespread this genomic architecture may be among the extant species conifers (Pinophyta). We used comparative analyses assess patterns abundance, diversity, distribution NLR genes. Chromosome-level whole genome assemblies high-density linkage maps Pinaceae, Cupressaceae, Taxaceae, other gymnosperms were scanned for using existing customized pipelines. The discovered mapped across chromosomes groups analyzed phylogenetically evolutionary history. Conifer genomes characterized by dense genes, highly localized on one chromosome. These rich TNL-encoding which seem have formed through multiple tandem duplication events. In contrast angiosperms nonconiferous gymnosperms, clustering ubiquitous conifers. NLR-dense regions likely influence part plant's resistance, informing our understanding adaptation biotic stress development genetic resources breeding.

Language: Английский

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Ripening and rot: How ripening processes influence disease susceptibility in fleshy fruits

Journal of Integrative Plant Biology, Journal Year: 2024, Volume and Issue: 66(9), P. 1831 - 1863

Published: July 17, 2024

Fleshy fruits become more susceptible to pathogen infection when they ripen; for example, changes in cell wall properties related softening make it easier pathogens infect fruits. The need high-quality fruit has driven extensive research on improving resistance important crops such as tomato (Solanum lycopersicum). In this review, we summarize current progress understanding how during ripening affect by pathogens. These physical barriers that limit entry, the epidermis and its cuticle, along with other defenses growth, preformed induced defense compounds. plant immune system also protects recognizing initiating responses involving reactive oxygen species production, mitogen-activated protein kinase signaling cascades, jasmonic acid, salicylic ethylene, abscisic acid signaling. phytohormones regulate an intricate web of transcription factors (TFs) activate mechanisms, including expression pathogenesis-related genes. tomato, regulators, RIPENING INHIBITOR NON_RIPENING, not only but influence against Moreover, members ETHYLENE RESPONSE FACTOR (ERF) family play pivotal distinct roles defense, different being regulated phytohormones. We discuss interaction ripening-related defense-related TFs Mediator complex. As processes climacteric non-climacteric share many similarities, these have broad applications across fruiting crops. Further individual contributions ERFs will inform efforts diminish disease susceptibility ripe fruit, satisfy growing demand decrease food waste economic losses.

Language: Английский

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What NLR you recognizing? Predicted binding affinities- and energies may be used to identify novel NLR-effector interactions

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 27, 2024

Abstract Nucleotide binding Leucine-rich repeat (NLR) proteins play a crucial role in effector recognition and activation of Effector triggered immunity plants following pathogen infection. Advances genome sequencing have led to the identification myriad NLRs numerous agriculturally important plant species. However, deciphering which NLR recognize specific effectors remains challenge. Predicting NLR-effector interactions silico would provide more targeted approach for experimental validation, critical elucidating function, advancing our understanding NLR-triggered immunity. In this study, protein complex structures were predicted using AlphaFold2-Multimer all experimentally validated interactions. Binding affinities– energies 97 machine learning models from Area-affinity. We show that with an AlphaFold confidence score > 0.42 acceptable accuracy, can be used investigate . affinities 58 complexes ranged between –8.5 –10.6 log(K), –11.8 –14.4 kcal/mol, depending on Area-Affinity model used. For 2427 “forced” complexes, these estimates showed larger variability, enabling novel 99% accuracy Ensemble model. The narrow range energies– true suggest change Gibbs free energy, thus conformational change, is required activation. This first study method predicting interactions, applicable plant-pathogen Finally, NLR-Effector Interaction Classification (NEIC) resource streamline research efforts by identifying providing resistance against pathogens,

Language: Английский

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Identifying nucleotide-binding leucine-rich repeat receptor and pathogen effector pairing using transfer-learning and bilinear attention network

Bioinformatics, Journal Year: 2024, Volume and Issue: 40(10)

Published: Sept. 27, 2024

Nucleotide-binding leucine-rich repeat (NLR) family is a class of immune receptors capable detecting and defending against pathogen invasion. They have been widely used in crop breeding. Notably, the correspondence between NLRs effectors (CNE) determines applicability effectiveness NLRs. Unfortunately, CNE data very scarce. In fact, we've found substantial 91 291 confirmed via wet experiments bioinformatics methods but only 387 CNEs are recognized, which greatly restricts potential application

Language: Английский

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Patterns of presence–absence variation of NLRs across populations of Solanum chilense are clade‐dependent and mainly shaped by past demographic history

New Phytologist, Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 24, 2024

Summary Understanding the evolution of pathogen resistance genes (nucleotide‐binding site‐leucine‐rich repeats, NLRs) within a species requires comprehensive examination factors that affect gene loss and gain. We present new reference genome Solanum chilense , which leads to an increased number more accurate annotation NLRs. Using target capture approach, we quantify presence–absence variation (PAV) NLR loci across 20 populations from different habitats. build rigorous pipeline validate identification PAV NLRs then show is larger than between populations, suggesting maintenance diversity linked population dynamics. The amount appears not be correlated with presence in clusters genome, but rather past demographic history species, diverging (smaller) at distribution edges. Finally, using redundancy analysis, find limited evidence being environmental gradients. Our results suggest random processes (genetic drift demography) weak positive selection for local adaptation shape single nucleotide polymorphism levels outcrossing plant high diversity.

Language: Английский

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The Exceptionally Large Genomes of the Fabeae Tribe: Comparative Genomics and Applications in Abiotic and Biotic Stress Studies

Agriculture, Journal Year: 2023, Volume and Issue: 14(1), P. 77 - 77

Published: Dec. 30, 2023

The Fabeae tribe comprises five legume genera, which include some of the most ancient and important crops, like peas, lentils, faba beans. Biotic environmental stresses are major threats to stable high productivity crops. use omics resources can provide breeders with tools needed develop new crop varieties in a more efficient sustainable way. However, genomic efforts on crops have lagged behind compared other species, mainly due their large genome size repeat content. first annotated chromosome-level reference assembly was published for pea (Pisum sativum cv. Caméor) 2019. Since then, many been made sequence species from this tribe. Currently, 17 genomes available scientific community; them at chromosome level. Fundamental knowledge molecular breeding boosted resistance/tolerance against biotic abiotic by availability these recent genomes, especially Caméor genome. This review provides comparison an overview accomplishments application stress research.

Language: Английский

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Patterns of presence-absence variation of NLRs across populations ofSolanum chilenseare clade-dependent and mainly shaped by past demographic history

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Oct. 17, 2023

Abstract Understanding the evolution of pathogen resistance genes (nucleotide-binding site-leucine-rich repeats, also known as NLRs) within a species requires comprehensive examination factors that affect gene loss and gain. We present new reference genome Solanum chilense , leads to an increased number more accurate annotation NLRs. Next, using target-capture approach, we quantify presence-absence variation (PAV) NLR loci across 20 populations from different habitats. build rigorous pipeline validate identification PAV NLRs, then show is larger than between populations, suggesting maintenance diversity linked population dynamics. Furthermore, amount not correlated with presence in clusters genome, but rather past demographic history species, NLRs diverging at distribution edges smaller sizes. Finally, redundancy analysis, find limited evidence being environmental gradients. Our results contradict classic assumptions important selective role for suggest driven by random processes (and weak selection) outcrossing plant high nucleotide diversity.

Language: Английский

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