An NLR paralog Pit2 generated from tandem duplication of Pit1 fine-tunes Pit1 localization and function

Yuying Li, Qiong Wang, Huimin Jia, Kazuya Ishikawa, Ken-ichi Kosami, Takahiro Ueba, Atsumi Tsujimoto, Miki Yamanaka, Yasuyuki Yabumoto, Daisuke Miki, Eriko Sasaki, Yoichiro Fukao, Masayuki Fujiwara, Takako Kaneko-Kawano, Li Tan, Chojiro Kojima, Rod A. Wing, Alfino Sebastian, Hideki Nishimura, Fumi Fukada, Qingfeng Niu, Motoki Shimizu, Kentaro Yoshida, Ryohei Terauchi, Ko Shimamoto and Yoji Kawano ()
Additional contact information
Yuying Li: Chinese Academy of Agricultural Sciences
Qiong Wang: Chinese Academy of Sciences
Huimin Jia: Jiangxi Agricultural University
Kazuya Ishikawa: Chinese Academy of Sciences
Ken-ichi Kosami: Chinese Academy of Sciences
Takahiro Ueba: Nara Institute of Science and Technology
Atsumi Tsujimoto: Nara Institute of Science and Technology
Miki Yamanaka: Nara Institute of Science and Technology
Yasuyuki Yabumoto: Nara Institute of Science and Technology
Daisuke Miki: Chinese Academy of Sciences
Eriko Sasaki: Kyushu University
Yoichiro Fukao: Ritsumeikan University
Masayuki Fujiwara: Ltd.
Takako Kaneko-Kawano: Ritsumeikan University
Li Tan: Chinese Academy of Sciences
Chojiro Kojima: Yokohama National University
Rod A. Wing: University of Arizona
Alfino Sebastian: Okayama University
Hideki Nishimura: Okayama University
Fumi Fukada: Okayama University
Qingfeng Niu: Anhui Agricultural University, Research Centre for Biological Breeding Technology
Motoki Shimizu: Iwate Biotechnology Research Center
Kentaro Yoshida: Kyoto University
Ryohei Terauchi: Iwate Biotechnology Research Center
Ko Shimamoto: Nara Institute of Science and Technology
Yoji Kawano: Chinese Academy of Sciences

Nature Communications, 2024, vol. 15, issue 1, 1-17

Abstract: Abstract NLR family proteins act as intracellular receptors. Gene duplication amplifies the number of NLR genes, and subsequent mutations occasionally provide modifications to the second gene that benefits immunity. However, evolutionary processes after gene duplication and functional relationships between duplicated NLRs remain largely unclear. Here, we report that the rice NLR protein Pit1 is associated with its paralogue Pit2. The two are required for the resistance to rice blast fungus but have different functions: Pit1 induces cell death, while Pit2 competitively suppresses Pit1-mediated cell death. During evolution, the suppression of Pit1 by Pit2 was probably generated through positive selection on two fate-determining residues in the NB-ARC domain of Pit2, which account for functional differences between Pit1 and Pit2. Consequently, Pit2 lost its plasma membrane localization but acquired a new function to interfere with Pit1 in the cytosol. These findings illuminate the evolutionary trajectory of tandemly duplicated NLR genes after gene duplication.

Date: 2024
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DOI: 10.1038/s41467-024-48943-5

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