AmirAli Toghani

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† Authors contributed equally to this work.
* Corresponding author(s).

Papers

AI-guided discovery of atypical protein assemblies

AmirAli Toghani†, Benjamin A. Seager†, Yu Sugihara, Lisa-Marie Roijen, Juan M. Azcue, Maián Garro, Maryam Sargolzaei, Ioanna Morianou, Adeline Harant, Sam Gallop, Jiorgos Kourelis, Dan MacLean, Mauricio P. Contreras, Sophien Kamoun*, Daniel Lüdke*

bioRxiv2026

A helper NLR channels organellar calcium to trigger plant immunity

Tarhan Ibrahim†, Freddie J. King†, AmirAli Toghani, Luyao Wang, Saskia Jenkins, Enoch Lok Him Yuen, Hung-Yu Wang, Cristina Vuolo, Nick Eilmann, Vanda Adamkova, Khong-Sam Chia, Baptiste Castel, Jonathan D. G. Jones, Philip Carella, Chih-Hang Wu, Jiorgos Kourelis*, Sophien Kamoun*, and Tolga O. Bozkurt*

Science2026

A broad-host-range Rhizobium rhizogenes strain enables transient expression across diverse crops and establishes functional assays in faba bean

Freddie King†, Juan Carlos Lopez-Agudelo†, Christopher Stephens, May Htet Aung, Tarhan Ibrahim, Enoch Lok Him Yuen, Ao Chen, Nick Moritz Eilmann, Saskia Jenkins, Cristina Vuolo, Yueh-Ning Swee, Wei-Jia Liu, Samuel Bruty, AmirAli Toghani, Chih-Horng Kuo, Erh-Min Lai, Jiorgos Kourelis, Lida Derevnina*, Chih-Hang Wu*, Tolga O. Bozkurt*

bioRxiv2026

The autoactivity of tomato helper NLR immune proteins of the NRC clade is unaltered in prf mutants of Nicotiana benthamiana

Daniel Lüdke, Hsuan Pai, AmirAli Toghani, Adeline Harant, Chih-Hang Wu, Sophien Kamoun*

Plant Physiology2025

A conserved small RNA-generating gene cluster undergoes sequence diversification and contributes to plant immunity

Li Feng†, Yingnan Hou†, AmirAli Toghani, Zhixue Wang, Bozeng Tang, Nicola Atkinson, Hui Li, Yue Qiao, Yan Wang, Jian Hua, Jixian Zhai, Wenbo Ma*

bioRxiv2025

Can AI modelling of protein structures distinguish between sensor and helper NLR immune receptors?

AmirAli Toghani, Raoul Frijters, Tolga O. Bozkurt, Ryohei Terauchi, Sophien Kamoun*, Yu Sugihara*

New Phytologist2025

An effector from the potato late blight pathogen bridges ENTH-domain protein TOL9a to an activated helper NLR to suppress immunity

Jogi Madhukprakash, AmirAli Toghani, Hsuan Pai, Madia Harvey, Adam R. Bentham, Benjamin A. Seager, Enoch Lok Him Yuen, Juan Carlos De la, David M. Lawson, Clare E. M. Stevenson, Angel Vergara-Cruces, Lida Derevnina, Tolga O. Bozkurt, Mark J. Banfield, Sophien Kamoun*, Mauricio P. Contreras*

bioRxiv2025

A root-specific NLR network mediates immune signaling of resistance genes against plant parasitic nematodes

Daniel Lüdke, Toshiyuki Sakai, Jiorgos Kourelis, AmirAli Toghani, Hiroaki Adachi, Andres Posbeyikian, Raoul Frijters, Hsuan Pai, Adeline Harant, Karin Ernst, Martin Ganal, Adriaan Verhage, Chih-Hang Wu, Sophien Kamoun*

The Plant Cell2025

Helper NLR immune protein NRC3 evolved to evade inhibition by a cyst nematode virulence effector

Yu Sugihara, Jiorgos Kourelis, Mauricio P Contreras, Hsuan Pai, Adeline Harant, Muniyandi Selvaraj, AmirAli Toghani, Claudia Martinez-Anaya*, Sophien Kamoun*

PLOS Genetics2025

A hierarchical immune receptor network in lettuce reveals contrasting patterns of evolution in sensor and helper NLRs

Hsuan Pai, Toshiyuki Sakai, Andres Posbeyikian, Raoul Frijters, Yu Sugihara, Mauricio P Contreras, Jiorgos Kourelis, Hiroaki Adachi, Sophien Kamoun*, AmirAli Toghani*

bioRxiv2025

A disease resistance protein triggers oligomerization of its NLR helper into a hexameric resistosome to mediate innate immunity

Jogi Madhuprakash*, AmirAli Toghani, Mauricio P Contreras, Andres Posbeyikian, Jake Richardson, Jiorgos Kourelis, Tolga O. Bozkurt, Michael W Webster*, Sophien Kamoun*

Science Advances2024

Activation of plant immunity through conversion of a helper NLR homodimer into a resistosome

Muniyandi Selvaraj, AmirAli Toghani, Hsuan Pai, Yu Sugihara, Jiorgos Kourelis, Enoch Lok Him Yuen, Tarhan Ibrahim, He Zhao, Rongrong Xie, Abbas Maqbool, Juan Carlos De la Concepcion, Mark J Banfield, Lida Derevnina, Benjamin Petre, David M Lawson, Tolga O. Bozkurt, Chih-Hang Wu, Sophien Kamoun*, Mauricio P Contreras*

PLOS Biology2024

Subfunctionalization of NRC3 altered the genetic structure of the Nicotiana NRC network

Ching-Yi Huang, Yu-Seng Huang, Yu Sugihara, Hung-Yu Wang, Lo-Ting Huang, Juan Carlos Lopez-Agudelo, Yi-Feng Chen, Kuan-Yu Lin, Bing-Jen Chiang, AmirAli Toghani, Jiorgos Kourelis, Chun-Hsiung Wang, Lida Derevnina, Chih-Hang Wu*

PLOS Genetics2024

REVIEW: NLR receptors in plant immunity: making sense of the alphabet soup

Mauricio P Contreras*, Daniel Lüdke, Hsuan Pai, AmirAli Toghani, Sophien Kamoun*

EMBO reports2023

Functional diversification of a wild potato immune receptor at its center of origin

Yerisf C Torres Ascurra, Lisha Zhang, AmirAli Toghani, Chenlei Hua, Nandeesh Jalahalli Rangegowda, Andres Posbeyikian, Hsuan Pai, Xiao Lin, Pieter J Wolters, Doret Wouters, Reinhoud de Blok, Niels Steigenga, Maxence JM Paillart, Richard GF Visser, Sophien Kamoun, Thorsten Nürnberger*, Vivianne GAA Vleeshouwers*

Science2023

Resurrection of plant disease resistance proteins via helper NLR bioengineering

Mauricio P Contreras, Hsuan Pai, Muniyandi Selvaraj, AmirAli Toghani, David M Lawson, Yasin Tumtas, Cian Duggan, Enoch Lok Him Yuen, Clare EM Stevenson, Adeline Harant, Abbas Maqbool, Chih-Hang Wu, Tolga O. Bozkurt, Sophien Kamoun*, Lida Derevnina*

Science Advances2023

An atypical NLR protein modulates the NRC immune receptor network in Nicotiana benthamiana

Hiroaki Adachi*, Toshiyuki Sakai, Adeline Harant, Hsuan Pai, Kodai Honda, AmirAli Toghani, Jules Claeys, Cian Duggan, Tolga O. Bozkurt, Chih-hang Wu*, Sophien Kamoun*

PLOS Genetics2023

Protocols

Phylogenomics of Plant NLR Immune Receptors to Identify Functionally Conserved Sequence Motifs

Toshiyuki Sakai, AmirAli Toghani, Hiroaki Adachi*

Bio-protocol2024

AmirAli Toghani

Papers

AI-guided discovery of atypical protein assemblies

A helper NLR channels organellar calcium to trigger plant immunity

A broad-host-range Rhizobium rhizogenes strain enables transient expression across diverse crops and establishes functional assays in faba bean

The autoactivity of tomato helper NLR immune proteins of the NRC clade is unaltered in prf mutants of Nicotiana benthamiana

A conserved small RNA-generating gene cluster undergoes sequence diversification and contributes to plant immunity

Can AI modelling of protein structures distinguish between sensor and helper NLR immune receptors?

An effector from the potato late blight pathogen bridges ENTH-domain protein TOL9a to an activated helper NLR to suppress immunity

A root-specific NLR network mediates immune signaling of resistance genes against plant parasitic nematodes

Helper NLR immune protein NRC3 evolved to evade inhibition by a cyst nematode virulence effector

A hierarchical immune receptor network in lettuce reveals contrasting patterns of evolution in sensor and helper NLRs

A disease resistance protein triggers oligomerization of its NLR helper into a hexameric resistosome to mediate innate immunity

Activation of plant immunity through conversion of a helper NLR homodimer into a resistosome

Subfunctionalization of NRC3 altered the genetic structure of the Nicotiana NRC network

REVIEW: NLR receptors in plant immunity: making sense of the alphabet soup

Functional diversification of a wild potato immune receptor at its center of origin

Resurrection of plant disease resistance proteins via helper NLR bioengineering

An atypical NLR protein modulates the NRC immune receptor network in Nicotiana benthamiana

Posters

AI modelling of protein structures can distinguish between sensor and helper NLR immune receptors

A hierarchical immune receptor network in lettuce reveals contrasting patterns of evolution in sensor and helper NLRs

Evolutionary diversification of protein-protein interaction interfaces: A case study on an NLR immune receptor network

What is driving the diversification of the N-terminal α1-helix of NRC helper NLRs?

Phylogenetically conserved TIR-NLR proteins induce transcriptional reprogramming

Protocols

Phylogenomics of Plant NLR Immune Receptors to Identify Functionally Conserved Sequence Motifs

Datasets

AlphaFold 3 hexameric resistosome models for 637 NRC-clade NLR proteins from Solanaceae

Harmonized genome annotation of 346 Solanaceae species reveals 197,834 NLR immune receptors

Deep-learning-based annotation of 230 superasterid genomes reveals a harmonized dataset of 91,366 NLRs

Functional annotation of 180 RefSeq reference plant proteomes reveals a dataset of 113,684 NLR proteins

AlphaFold 3 predicted NLR resistosome structures

NLRome dataset from 124 genomes of plants in the Solanaceae family