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Department of Plant Biology
University of Minnesota
250 Biological Science Center
1445 Gortner Ave.
St. Paul, MN 55108

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Fumiaki Katagiri

Associate Professor, Department of Plant Biology
Ph.D., Rockefeller University, 1991

Systems biology of plant disease resistance

Contact Information

Mailing Address:

Dr. Fumiaki Katagiri
Department of Plant Biology
University of Minnesota
326 Cargill Building
1500 Gortner Avenue
St. Paul, MN 55108

Research Interests

I. Plant Immune Network

A major type of plant defense against pathogen is inducible defense: i.e., defense mechanisms are turned on upon recognition of pathogen attack. Research in my group is directed towards understanding (1) how plants recognize pathogen attack and (2) how this recognition leads to induction of coordinated responses in plants. We use Arabidopsis thaliana and its bacterial pathogen Pseudomonas syringae as a model to study these problems. Plants recognize pathogen attack by detecting molecules delivered or derived from pathogens outside or inside the cell. Recognizing pathogen molecules outside the plant cell is mediated by membrane receptors, typically receptor-like kinases: the molecules derived from pathogens are called microbe-associated molecular patterns (MAMPs), the MAMP receptors are called pattern-recognition receptors (PRRs), and the resistance triggered by this recognition is called pattern-triggered immunity (PTI). Recognition of pathogen molecules inside the plant cell is mediated by resistance (R) proteins, typically nucleotide binding – leucine rich repeat proteins (NB-LRRs): the molecules delivered by pathogens are called effectors, and the resistance triggered by this recognition is called effector-triggered immunity (ETI). We are interested in a network of molecules that enables PTI and ETI: how are the components and connections of the network organized?; how is the behavior of the network controlled?

1. How plants recognize pathogen attack. To gain insights in how R proteins recognize effectors and how this recognition initiates signaling, we identified a number of proteins that form complexes with R proteins.  This study revealed that at least some R proteins and PRRs form complexes together in lipid raft regions of the plasma membrane, suggesting interactions between PTI and ETI at the very beginning of the processes.
2. How this recognition leads to induction of coordinated responses in plants. Our ultimate goal in this area is to understand the signaling mechanisms well enough, so that we will be able to build a quantitative model for this signaling network on computer. Signaling networks for PTI and ETI are overlapped and have highly interconnected architecture. In such a network, memberships and the order of particular components are not clearly determined. Therefore, a conventional approach of reductionism, i.e., isolating a part based on an assumption of independence from the other parts, does not work well for the purpose of elucidate the network property.  We have demonstrated that two strategies are effective in studying such a complex network: perturb a part of the network and collect information from many different points of the network at once; perturb multiple parts of the network simultaneously so that large effects of perturbations can be observed, and then deconvolute the effects of and interactions among the perturbed parts. In this way, we found that at least some PTI and ETI extensively share the network components but use the network quite differently, that this network has a strong tendency to compensate loss of part of the network and that this compensation is achieved by rerouting signal flows in the network (a backup function instead of simple redundancy).  We are combining these two strategies to elucidate the detailed organization and dynamics of the network.
3. Computational biology and Bioinformatics.   We are integrating computational approaches to experimental approaches to facilitate our study.   The small-scale microarray we developed for mRNA expression profiling uses a model-based statistics and a novel normalization method to enable accurate and inexpensive measurement.   We apply nonlinear multivariate analysis to infer the signaling network topology. 

II. Wheat Stem Rust Resistance

Stem rust disease had been reasonably controlled in wheat thanks to breeding of R genes.  However, a new isolate, Ug99, found in East Africa in 1999, can break resistance conferred by most R genes that have so far been deployed among wheat varieties.  Spores of rust fungi travel long distance: by now Ug99-derivatives have spread to Iran, and eventual pandemic is likely inevitable.  This would cause a devastating effect in developing countries where wheat is a staple and where farmers cannot afford fungicides.  We will isolate effector genes first, isolate R genes recognizing the effector genes from various cereal species, and use the R genes to engineer stem rust-resistant wheat varieties.  In this way, we will deliver genetic solutions to Ug99.

Recent Publications (refereed, since 2000)

Nimchuk, Z., Marois, E., Kjemtrup, S., Leister, R. T., Katagiri, F., and Dangl, J. (2000) “Phytopathogen effector molecules from Pseudomonas syringae function at the host plant cell plasma membrane and are targeted via eukaryotic fatty acylation.” Cell 101, 353-363. 

Leister, R. T. and Katagiri, F. (2000) “A resistance gene product of the nucleotide binding site – leucine rich repeats class can form a complex with bacterial avirulence proteins in vivo.” Plant J. 22, 345-354.

Chen, Z., Kloek, A. P., Boch, J., Katagiri, F., and Kunkel, B. N. (2000) “The Pseudomonas syringae avrRpt2 gene product promotes pathogen virulence from inside plant cells.” Molecular Plant-Microbe Interactions 13, 1312-1321.

Tao, Y., Yuan, F., Leister, T., Ausubel, F. M., and Katagiri, F. (2000) “Mutational analysis of the Arbidopsis NBS-LRR resistance gene RPS2” Plant Cell 12, 2541-2554.

Chen, W., Provart, N., Glazebrook, J., Katagiri, F., Chang, H.-S., Eulgem, T., Mauch, F., Luan, S., Zou, G., Whitham, S., Budworth, P., Tao, Y., Xie, Z., Chen, X., Lam, S., Kreps, J., Harper, J., Si-Ammour, A., Mauch-Mani, B., Heinlein, M., Kobayashi, K., Hohn, T., Dangl, J., Wang, X., and Zhu, T. (2002) “Expression Profile Matrix of Arabidopsis Transcription Factor Genes implies Their Putative Functions in Response to Environmental Stresses” Plant Cell 14, 559-574. 

Goff, S. A., Ricke, D., Lan, T. H., Presting, G., Wang, R., Dunn, M., Glazebrook, J., Sessions, A., Oeller, P., Varma, H., Hadley, D., Hutchison, D., Martin, C., Katagiri, F., Lange, B. M., Moughamer, T., Xia, Y., Budworth, P., Zhong, J., Miguel, T., Paszkowski, U., Zhang, S., Colbert, M., Sun, W. L., Chen, L., Cooper, B., Park, S., Wood, T. C., Mao, L., Quail, P., Wing, R., Dean, R., Yu, Y., Zharkikh, A., Shen, R., Sahasrabudhe, S., Thomas, A., Cannings, R., Gutin, A., Pruss, D., Reid, J., Tavtigian, S., Mitchell, J., Eldredge, G., Scholl, T., Miller, R. M., Bhatnagar, S., Adey, N., Rubano, T., Tusneem, N., Robinson, R., Feldhaus, J., Macalma, T., Oliphant, A., Briggs, S. (2002) “A draft sequence of the rice genome (Oryza sativa L. ssp. japonica)” Science 296, 92-100.

Sessions, A., Burke, E., Presting, G., Aux, G., McElver, J., Patton, D. Dietrich, B., Ho, P., Bacwaden J., Ko, C., Clarke, J. D., Cotton D., Bullis, D., Snell, J., Miguel, T., Hutchison, D., Kimmerly, B., Nitzel, T., Katagiri, F., Glazebrook J., Law, M., and Goff, S. A. (2002) “A high-throughput Arabidopsis reverse genetics system” Plant Cell 14, 2985-2994. 

Wu, Y., Wood, M. D., Tao, Y., and Katagiri, F. (2003) “Direct delivery of bacterial avirulence proteins into resistant Arabidopsis protoplasts leads to hypersensitive cell death.” Plant J. 33, 131-137.

Tao, Y., Xie, Z., Chen, W., Glazebrook, J., Chang, H.-S., Han, B., Zhu, T., Zou, G., and Katagiri, F. (2003) “Quantitative nature of Arabidopsis responses during compatible and incompatible interactions with the bacterial pathogen Pseudomonas syringae.” Plant Cell15, 317-330. 

Glazebrook, J., Chen, W., Estes, B., Chang, H.-S., Nawrath, C., Metraux, J.-P., and Katagiri, F. (2003) “Topology of the Network Integrating Salicylate and Jasmonate Signal Transduction Derived from Global Expression Phenotyping” Plant J. 34, 217-228. 

Katagiri, F. and Glazebrook, J. (2003) “Local Context Finder (LCF) reveals multidimensional relationships among Arabidopsis mRNA expression profiles in response to pathogen infection.” Proc. Natl. Acad. Sci. USA 100, 10842-10847. 

Jin, P., Wood, M. D., Wu, Y., Xie, Z., and Katagiri, F. (2003) “Cleavage of the Pseudomonas syringae type III effector AvrRpt2 requires a host factor(s) common among eukaryotes and is important for AvrRpt2 localization in the host cell.” Plant Physiol 133, 1072-1082. 

Lee, C., Wood, M. D., Ng, K., Andersen C., Liu, Y., Luginbuhl, P., Spraggon, G., and Katagiri, F. (2004) “Crystal structure of the Type III effector AvrB from Pseudomonas syringae” Structure 12, 487-494.

Sato, M., Mitra, R. M., Coller, J., Wang, D., Spivey, N. W., Dewdney, J., Denoux, C., Glazebrook, J., and Katagiri, F. (2007) “A high performance, small-scale microarray for expression profiling of many samples in Arabidopsis-pathogen studies” Plant J. 49, 565-577. 

van Leeuwen, H., Kliebenstein, D. J., West, M. A. L., Kim, K., van Poecke, R., Katagiri, F., Michelmore, R. W., Doerge, R. W., St. Clair, D. A. (2007) “Natural variation among Arabidopsis thaliana accessions for transcriptome response to exogenous salicylic acid.” Plant Cell 19, 2099-2110. 

van Poecke, R. M. P., Sato, M., Lenarz-Wyatt, L., Weisberg, S., and Katagiri, F.  (2007) “Natural variation in RPS2-mediated resistance among Arabidopsis accessions: correlation between gene expression profiles and phenotypic responses.” Plant Cell 19, 4046-4060. 

Tsuda, K., Sato, M., Glazebrook, J., Cohen, J. D., and Katagiri, F. (2008) “Interplay between MAMP-triggered and SA-mediated defense responses.” Plant J. 53, 763-775. 

Wang, L., Mitra, R. M., Hasselmann, K. D., Sato, M., Lenarz-Wyatt, L. M., Cohen, J. D., Katagiri, F., and Glazebrook, J. (2008) “The Genetic Network Controlling the Arabidopsis Transcriptional Response to Pseudomonas syringae pv. maculicola: Roles of Major Regulators and the Phytotoxin Coronatine” Mol. Plant-Microbe Interaction 21, 1408-1420. 

Foley, J. W. and Katagiri, F. (2008) “Unsupervised reduction of random noise in complex data by a row-specific, sorted principal component-guided method” BMC Bioinformatics 9, 508. 

Qi, Y. and Katagiri, F. (2009) “Purification of low-abundance Arabidopsis plasma-membrane protein complexes and identification of their component candidates” Plant J., 57(5), 932-944.

Wang, L., Tsuda, K., Sato, M., Cohen, J.D., Katagiri, F., and Glazebrook, J.  (2009) “Arabidopsis CaM binding protein CBP60g contributes to MAMP-induced SA accumulation and is involved in disease resistance against Pseudomonas syringae.”  PLoS Pathogens 5(2), e1000301.