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Phone: (612) 625-1234
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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

Office: 326 Cargill Center for Microbial and Plant Genomics
Phone: 612-624-5195
Fax: 612-624-6264
E-mail: katagiri@umn.edu

Research Interests

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. The type of resistance we mainly study is called resistance ( R ) gene-mediated resistance. R gene-mediated resistance is usually strong and based on highly specific recognition of particular pathogen factors.

1. How plants recognize pathogen attack.

   We try to elucidate how exactly this molecular recognition of pathogen factors is mediated and how signaling of this recognition is initiated by R gene products. We are also interested in determining the repertoire of recognition specificity defined by the R gene family (NB-LRR genes) in Arabidopsis. Furthermore, we are investigating whether members of the R gene family have any roles in other types of resistance mechanisms.   We employ genetic, reverse-genetic, biochemical, genomic, and proteomic approaches for these objectives.

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. However, the topology of the signaling network is complex, and information we can obtain by conventional approaches is quite limited. Our major way to collect data from the signaling system is combining a large scale reverse genetics and massive, quantitative phenotyping enabled by mRNA expression profiling. Based on this type of data, we will elucidate complex relationships among the components involved in the network using a computational approach. We are also tapping into natural variation among populations of Arabidopsis using genomic technologies to discover novel components of the network.   Furthermore, we are trying to shut down the entire signaling network and reconstitute it with one component at a time - with this technology, we will be able to collect data that are much easier to interpret for the purpose of elucidating the signaling network.

3. Computational biology and Bioinformatics.  

   We are integrating computational approaches to experimental approaches to facilitate our discovery.The small-scale microarray we developed for mRNA expression profiling uses a model-based statistics and a novel normalization method to enable accurate measurement.We are building a database that allows recording and statistical analysis of metadata, as well as the mRNA expression profiles and other experimental data. We apply nonlinear multivariate analysis to infer the signaling network topology.We are developing a rapid QTL mapping method for the purpose of discovering novel components of the network.

Selected Publications

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 Æ 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 Cell 15, 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. 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 (2003).

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

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. “Natural variation among Arabidopsis thaliana accessions for transcriptome response to exogenous salicylic acid.” Plant Cell, in press.