ViPS Invited Seminar May 2017

Hirofumi Nakagami, Max Planck Cologne, Germany

Date: 17th May 2017

Time: 13:15

Title: Multi-omic strategies to understand plant immune system

Location: Lecture room 4, Viikki B building, Latokartanonkaari 7-9

Host: Michi Wrzaczek

Abstract: The infection of plants by pathogens is causing a considerable economic loss to agricultural industries. Recent studies estimated that the global yield loss due to biotic stresses averages over 23 percent of the estimated attainable yield across major cereals. An understanding of the fundamental mechanisms underlying disease resistance processes is expected to provide novel ideas for improving the current situation. During the last several decades, extensive analyses revealed that plants utilize a two-branched immune system for defense against pathogens. In the first branch, transmembrane pattern recognition receptors (PRR) are used to recognize and respond to slowly evolving microbe-associated molecular patterns (MAMP). In the second branch, either a direct or an indirect recognition of the pathogen through disease-resistance (R) proteins is used for response to pathogen virulence factors. The R-gene mediated resistance has been widely used in crop improvement. However, the resistance is pathogen race-specific and, frequently, a rapid breakdown of the resistance has been reported. Consequently, alternative approaches to provide a broad-spectrum, durable resistance in crops are highly desirable. Meanwhile, several studies have implied that manipulation of the PRR-mediated immune system can be a smart strategy to enhance the broad-spectrum resistance. While extensive genetic screens successfully identified a number of PRRs and components which affect abundance and maturation of PRRs, signal transduction mechanisms that lead to defense responses is thus far limited. This partly stems from limitations of forward genetics caused by lethality and/or genetic redundancy. Accordingly, we have established shotgun phosphoproteomics platform by which thousands of phosphopeptides can be identified and quantified from plant materials to dissect out poorly characterized signal transduction systems by monitoring phosphorylation dynamics. By using Arabidopsis as a material, we could successfully identify novel components in plant immunity. Meanwhile, unsophisticated proteomics approaches often resulted in identification of too many potential regulators whose importance are uncertain. The comparative and evolutionary genomics/proteomics could be efficient approaches to elucidate fundamental components and systems that are broadly conserved across the plant kingdom. Therefore, we started to investigate whether emerging model organism liverworts Marchantia polymorpha can be used as new model system to understand plant immunity. Importantly, Marchantia genome has been reported to have highly streamlined architecture, with smaller gene families and less redundancy compared to higher plants. Analysis of Marchantia with simple gene networks is expected to facilitate exploring the fundamental components of plant immune system.

Hirofumi Nakagami's group focuses on establishing proteomics methods to analyze phosphorylation events in plants. By utilizing the established methods, we are attempting to dissect plant immune siganling pathways.

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Relevant publications:

Sugiyama N, Nakagami H, Mochida K, Daudi A, Tomita M, Shirasu K, Ishihama Y, “Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis”, Mol Syst Biol, 2008; 4: 193.

Nakagami H, Sugiyama N, Mochida K, Daudi A, Yoshida Y, Toyoda T, Tomita M, Ishihama Y, Shirasu K, “Large-scale comparative phosphoproteomics identifies conserved phosphorylation sites in plants”, Plant Physiol, 2010 Jul;153(3):1161-74.

Choudhary MK, Nomura Y, Wang L, Nakagami H, Somers DE, “Quantitative circadian phosphoproteomic analysis of Arabidopsis reveals extensive clock control of key components in physiological, metabolic and signaling pathways”, Mol Cell Proteomics, 2015 Aug;14(8):2243-60.

Bowman JL, Araki T, Arteaga-Vazquez MA, Berger F, Dolan L, Haseloff J, Ishizaki K, Kyozuka J, Lin S, Nagasaki H, Nakagami H, Nakajima K, Nakamura Y, Ohashi-Ito K, Sawa S, Shimamura M, Solano R, Tsukaya H, Ueda T, Watanabe Y, Yamato KT, Zachgo S, Kohchi T, “The naming of names: guidelines for gene nomenclature in Marchantia”, Plant Cell Physiol., 2016 Feb;57(2):257-61.

Yamada K, Yamaguchi K, Shirakawa T, Nakagami H, Mine A, Ishikawa K, Fujiwara M, Narusaka M, Narusaka Y, Ichimura K, Kobayashi Y, Matsui H, Nomura Y, Nomoto M, Tada Y, Fukao Y, Fukamizo T, Tsuda K, Shirasu K, Shibuya N, Kawasaki T, “The Arabidopsis CERK1-associated kinase PBL27 connects chitin perception to MAPK activation”, EMBO J., 2016 Nov 15;35(22):2468-2483.

Yamada K, Saijo Y, Nakagami H, Takano Y, “Regulation of sugar transporter activity for antibacterial defense in Arabidopsis” Science, 2016 Dec 16;354(6318):1427-1430.