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Soybean Proteomics

EMSL Project ID


The USA is the world's largest producer of soybean (Glycine max) according to the UN food and agriculture organization with a production of 83.9 million metric tons per year. Soybean is an important crop for animal feed, oil and, more recently, for biodiesel production. In recognition of this latter fact, the Department of Energy-Joint Genome Institute recently completed and published the sequence of the soybean genome; (

The availability of the genome sequence now enables detailed proteomic analysis of soybean. Over the past few years, we have developed a close and productive collaboration with the PNNL EMSL laboratory. This has resulted in the awarding of two grants to support this collaborative work. The first, funded by the National Science Foundation, continues our efforts to use a variety of functional genomic tools to characterize the response of soybean root hair cells to infection by the symbiotic, nitrogen fixing bacterium, Bradyrhizobium japonicum. Our work in this system has now established the soybean root hair as a model for studying single cell plant biology. Our second collaborative grant is funded by the Biological and Environmental Research Division of the Department of Energy. Again, this project utilizes our soybean root hair model system but specifically explores the cellular response to abiotic stress factors, namely heat and drought. Funds from both of these grants flow to EMSL researchers. This proposal seeks formal approval to continue this productive collaboration between EMSL and the University of Missouri.

The current project as three objectives:
1. Utilize proteomic approaches to examine the role of protein-protein complex formation, protein phosphorylation and histone modification in the regulatory circuitry controlling B. japonicum root hair infection.
2. Analyze proteomic and metabolomic changes in root hair cells under conditions of abiotic stress (i.e., heat and drought stress)
3. Develop and apply computational systems biology methods to study genes, proteins, non-coding RNAs, and pathways involved in root hair cell biology by integrating dissimilar experimental data.

The project will make use of the advanced proteomic expertise and instrumentation available at EMSL. We also hope to expand our collaboration to include the advanced fluorescence microscopy capabilities at EMSL. Finally, as a comparison to the proteomic analysis, we plan to examine mRNA abundance in soybean tissues using the high throughput sequencing capabilities now present at EMSL.

Project Details

Project type
Large-Scale EMSL Research
Start Date
End Date


Principal Investigator

Gary Stacey
University of Missouri - Columbia

Team Members

Josef Batek Rios
University of Missouri - Columbia

Eirik Krogstad
Pacific Northwest National Laboratory

Dong Xu
University of Missouri - Columbia

Ronald Moore
Pacific Northwest National Laboratory

David Brown
Environmental Molecular Sciences Laboratory

Related Publications

Brechenmacher L, KK Hixson, M Libault, JT Aldrich, L Pasa-Tolic, and G Stacey. 2012. "Identification of soybean proteins from a single cell type: the root hair." PNNL-SA-86320, Pacific Northwest National Laboratory, Richland, WA. [Unpublished]
Brechenmacher L, TH Nguyen, KK Hixson, M Libault, JT Aldrich, L Pasa-Tolic, and G Stacey. 2012. "Identification of soybean proteins from a single cell type: The root hair." Proteomics 12(22):3365-3373. doi:10.1002/pmic.201200160
Joshi T, K Patil, MR Fitzpatrick, LD Franklin, Q Yao, JR Cook, Z Wang, M Libault, L Brechenmacher, B Valliyodan, X Wu, J Cheng, G Stacey, HT Nguyen, and D Xu. 2012. "Soybean Knowledge Base (SoyKB): a Web Resource for Soybean Translational Genomics." BMC Genomics 13:S15. doi:10.1186/1471-2164-13-S1-S15
Nguyen TH, L Brechenmacher, JT Aldrich, TRW Clauss, MA Gritsenko, KK Hixson, M Libault, K Tanaka, F Yang, Q Yao, L Pasa-Tolic, D Xu, HT Nguyen, and G Stacey. 2012. "Quantitative Phosphoproteomic Analysis of Soybean Root Hairs Inoculated with Bradyrhizobium japonicum." Molecular & Cellular Proteomics. MCP 11(11):1140-1155. doi:10.1074/mcp.M112.