Basic Immune System of Plants (Hirofumi Nakagami)
During the last several decades, extensive analyses revealed that plants utilize a two-branched immune system for defence against pathogens. In the first branch, transmembrane pattern recognition receptors (PRR), which are membrane-associated kinase or membrane-associated kinase interacting protein, are used to recognize and respond to slowly evolving pathogen-associated molecular patterns (PAMP). 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 (Effector).
While extensive genetic screens successfully identified a number of receptors and components which affect abundance and maturation of the receptors, signal transduction mechanisms that lead to defence responses is thus far limited. This partly stems from limitations of forward genetics caused by lethality and/or genetic redundancy. Accordingly, my group takes proteomics-based approaches to understand the basic framework of the plant immune system.
1. Phosphoproteomic dissection of PAMP-triggered immunity
Several studies indicated that distinct PRRs share downstream components to induce defence responses. To identify crucial components for PAMP-triggered immunity (PTI), we have been monitoring phosphoproteome dynamics upon different PAMP treatments.
One of the key requirements for successful posttranslational modification (PTM)-oriented proteomics is the establishment of efficient enrichment methods for posttranslationally modified peptides. We have developed a posttranslational modification (PTM)-oriented proteomics platform, with an emphasis on phosphorylation as this plays a significant role in early events of plant immune responses.
References and further reading
Matsui H, Nomura Y, Egusa M, Hamada T, Hyon GS, Kaminaka H, Watanabe Y, Ueda T, Trujillo M, Shirasu K, Nakagami H, “The GYF domain protein PSIG1 dampens the induction of cell death during plant-pathogen interactions”, PLoS Genetics, 13(10):e1007037 (2017)
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, Molecular & Cellular Proteomics, 14(8):2243-60 (2015)
Nakagami H, StageTip-based HAMMOC, an efficient and inexpensive phosphopeptide enrichment method for plant shotgun phosphoproteomics, Methods in Molecular Biology "Methods in Plant Proteomics", 1072:595-607 (2014)
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 Physiology, 153(3):1161-74 (2010)
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, Molecular Systems Biology, 4:193 (2008)
2. Immune system in the basal land plant Marchantia
The comparative and evolutionary genomics/proteomics are 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, a descendant of earliest land plants, 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 with flowering plants. Transformation and targeted genome modification techniques for Marchantia have been already established. Analysis of Marchantia with simple gene networks is expected to facilitate exploring the fundamental components of plant immune system.
References and further reading
Bowman JL, Kohchi T, Yamato KT, …, Nakagami H, … et al., “Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome”, Cell, 171(2):287-304.e15 (2017)