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Sixue Chen, Ph.D.

Assistant Professor of Botany

• Sixue Chen, Ph.D.

  Assistant Professor of Botany

  • Plant Secondary Metabolism and Proteomics
  • 438 Cancer & Genetics Research Complex
  • (352) 273-8330
  • schen@ufl.edu

  Biography

  My training as a plant biochemist started when I was admitted to the joint Ph.D. training program between East China Normal University and Shanghai Institute of Plant Physiology, Chinese Academy of Sciences. After receiving my Ph.D., I was awarded an Alexander-von-Humboldt fellowship to study the catalytic mechanism underlying peroxidase mediated hydroxyl radical production at University of Freiburg, Germany. In 1998, I was funded by Danish Research Council to study glucosinolate metabolism and transport at the Royal Veterinary and Agricultural University of Denmark. In 2001, I moved to Dr. Philip Rea's laboratory at University of Pennsylvania and focused my research on vacuolar proteomics (vacuomics) and ATP-binding cassette (ABC) transporters. I continued proteomics research and service during my tenure at the Danforth Center.
  My long-term goal in research is to understand the biochemical and cellular mechanisms underlying plant growth, development and interactions with the environment using large-scale functional genomics approaches as well as biochemistry, molecular biology and genetics tools. Only through a thorough understanding of how the plant system works, will it be possible to efficiently and effectively utilize the plant biofactory for the benefits of humanity and the environment.

  Education

  • Ph.D. Shanghai Institute of Plant Physiology & East China Normal University, 1996
  • M.S. East China Normal University, 1993
  • B.S. Harbin Normal University, 1991

  Ph.D. Dissertation Title: Plant plasma membrane transport systems and osmotic shock signal transduction in Dunaliella salina.

  Academic Positions

  • 2006- present Assistant Professor, Dept. of Botany, University of Florida, Gainesville, FL
  • 2003-06 Director of Proteomics and Mass Spectrometry Facility, Donald Danforth Plant Science Center, St. Louis, MO
  • 2001-03 Postdoctoral Research Associate & Manager of Proteomics Facilty, Leidy Laboratories, Dept. of Biology, University of Pennsylvania, Philadelphia, PA
  • 1998-01 Assistant Research Professor, Plant Biochemistry Laboratory & Center for Molecular Plant Physiology, The Royal Veterinary and Agricultural University, Denmark
  • 1997-98 Alexander-von-Humboldt Researcher, Biologie Institut, Albert-Ludwigs-Universrsitaet, Germany

  Research Interests / Major Research Achievements:

  Plants produce thousands of secondary metabolites that are closely related to human nutrition and health. These metabolites have been used as food, flavors, color dyes, poisons, perfumes, scented oils, industrial products and medicines. For example, approximately 1/4 of prescription drugs contain at least one chemical originally extracted from a plant. Plant secondary metabolites are of high chemical complexity and biological dynamics. A central question is why, how and where plants produce and store these compounds.
  Glucosinolates are a group of naturally occurring thioglucosides, present in important Brassica crops (e.g. oilseed rape, broccoli and cabbage) as well as in model plant Arabidopsis. Glucosinolate degradation products display diverse biological activities, including interaction with insects and herbivores, N/S nutrition and growth regulation. From a human perspective, glucosinolate metabolites account for the distinctive flavors of cabbage and condiments. Some of the degradation products, e.g. isothiocyanates exhibit anticarcinogenic properties. Glucosinolate biosynthetic pathway has been well studied in Arabidopsis using biochemical and reverse genetic tools. Preliminary studies have indicated that glucosinolate metabolism interacts with a number of pathways essential for plant growth, development and response to environmental factors. Research in the Chen laboratory is aimed at characterizing the regulatory and metabolic pathway networks involving glucosinolate metabolism using functional genomics and systems biology approaches. Detailed understanding of pathway interactions is essential for prediction/modeling and targeted engineering of plant secondary metabolites. The ultimate goal is to use the immense biosynthetic potential of plants as an efficient, environmentally friendly and renewable source of fine chemicals and pharmaceuticals for improvement of plant protection, human health and nutrition. Research projects include:

  • Signal transduction and regulatory pathways in glucosinolate metabolism
  • Interaction of glucosinolate metabolism with other metabolic pathways
  • Integration of “-omics” data and generation of gene-protein-metabolite networks
  • Systems biology of anticarcinogenic activities of glucosinolate degradation products
  • Development of tools for mining low abundance proteins and metabolites

  Present / Past Students

  Mengmeng Zhu (Ph.D.)
  Yan He (Ph.D.)
  Jason Hall (Undergraduate)
  Mark Jackson (Undergraduate)
  Shaojun Dai (Visiting Scholar, position: Professor at Northeast Forestry University)
  Sophie Alvarez (Postdoctorate, current position: Assistant manager at Danforth Center)

  Present Research

  Qualitative and quantitative proteomics in guard cell signaling and metabolism.
  Functional characterization of plant glucosinolate metabolic networks.

  Courses Taught:

  BOT 6508C Proteomics: Theory and Practice (graduate)
  GMS 6181 Genomics and Bioinformatics (graduate)
  BOT 5505  Intermediate Plant Physiology (graduate)
  BOT 3503 Physiology and Molecular Biology of Plants (undergraduate and graduate)
  BOT 3503L Laboratory for Physiology and Molecular Biology of Plants (undergraduate)

  Membership in Professional Organizations:

  • The Proteomics Society
  • American Society for Mass Spectrometry (ASMS)
  • Association of Biomolecular Resource Facilities (ABRF)
  • International Science Advisory Board, Plant Science Section
  • American Society for Plant Biology (ASPB)

  Grants received

  • 2007-11 NSF Genome Grant (Co-PI, Pending), Proteomics in maize root sensing and adaptation to nutrient deficiency, University of Florida.
  • 2002-06 NSF Genome Grant (Collaborator) Donald Danforth Plant Science Center
  • 1998-01 Danish Research Council Grant, Royal Veterinary and Agricultural University, Denmark

  Selected Publications

  Alvarez, S., He, Y., Chen, S. (2008) Comparative investigations of glucosinolate-myrosinase system in Arabidopsis suspension cells and hypocotyls. Plant Cell and Physiology (in press)

  Chen, S., Sánchez Fernández, R., Lyver, E.R., Dancis, A.,  Rea, P.A. (2007) Functional half molecule ABC transporters from Arabidopsis thaliana: The ATM subfamily. Journal of Biological Chemistry 282, 21561-21571.

  Yan, X.F., Chen, S. (2007) Regulation of plant glucosinolate metabolism. Planta 226, 1343-1352.

  Sarry, J.*, Chen, S.*, Collum, R., Liang, S., Peng, M., Lang, A., Yuan, C., Hippler, M., Rea P. (2007) Analysis of the vacuolar luminal proteome of yeast Saccharomyces cerevisiae.  FEBS Journal 274, 4287-4305.

  Dai, S., Yan, X.F., Chen, S. (2007) Proteomics of pollen development and germination. Journal of Proteome Research 6, 4556-4563.

  Jez, J.M., Schachtman, D.P., Berg, R.H., Taylor, C.G., Chen, S., Hicks, L.M.,  Jaworski, J.G., Smith, T.J., Nielsen, E., Pikaard, C.S. (2007) Developing a new interdisciplinary lab course for undergraduate and graduate students: Plant Cells and Proteins. Biochemistry and Molecular Biology Education  35, 410-415.

  Zhu, J., Alvarez, S., Marsh, E., LeNoble, M.E., Cho, I.J., Chen, S., Nguyen, H.T., Sivaguru, M., Wu, Y., Schachtman, D., Sharp, R.E. (2007) Changes in the Cell Wall Proteome in the Maize Primary Root in response to water deficit. II. Region-Specific Changes in the Water Soluble and Lightly Ionically-Bound Proteins. Plant Physiology  145, 1533-1548

  Chen, S., Harmon, A. (2006) Advances in plant proteomics. Proteomics 6, 5504-5516.

  Sheffield, J., Taylor, N., Fauquet, C., Chen, S. (2006) Cassava root proteome: protein identification and differential expression. Proteomics 6, 1588-1598 (Cover).

  Alvarez, S., Goodger, J., Marsh, E., Chen, S., Schachtman, D.P. (2006) The proteome of maize xylem sap and changes after drought stress. Journal of Proteome Research 5, 963-972.

  Chen, S. (2006) High throughput protein separation and mass spectrometry characterization. In Plant Biotechnology Application Guide, chapter 9. Chemical Industry Press, pp. 143-160.

  Chen, S. (2006) Rapid protein identification using direct infusion nanoelectro-spray ionization mass spectrometry. Proteomics 6, 16-25.

  Zhu, J., Chen, S., Asirvatham, V., Schachtman, D.P., Wu, Y., Sharp,  R.E. (2006) Cell wall proteome in the maize primary root elongation zone. I. Extraction and identification of water soluble and lightly ionically-bound proteins. Plant Physiology 140, 311-325.

  Herman, E.M., Rotter, K., Premakumar, R., Elwinger, G., Bae, R., King, L.E., Chen, S., Livingston, D.P. (2006) Additional freeze hardiness in wheat acquired by exposure to -3 oC is correlated with changes in physiology, structure, transcriptome and proteome. Journal of Experimental Botany 57, 3601-3618.

  Yan, X., Wang, Y., Zhang, Y., Yu, T., Ma, M., Ju, S., Chen, S. (2005) Tissue-specific and environmental regulation of camptothecin and 10-hydroxy-camptothecin levels in Camptotheca acuminate. Bot. Bull. Acad. Sin. 46, 325-331.

  Jez, J., Cahoon, B., Chen, S. (2004) Arabidopsis thaliana glutamate-cysteine ligase: Functional properties, kinetic mechanism and regulation of activity. Journal of Biological Chemistry 279, 33463-33470.

  Maathuis, F.J.M., Filatov, V., Herzyk, P., Krijger, G.C., Axelsen, K.B., Chen, S., Green, B.J., Li, Y., Madagan, K.L., Sánchez-Fernández, R., Forde, B.J., Palmgren, M.G., Rea, P.A., Williams, L.E., Sanders, D., Amtmann, A. (2003)  Transcriptome analysis of root transporters reveals participation of multiple gene families in the response to cation stress.  Plant Journal 35, 675-692.

  Rea, P.A., Sanchez-Fernandez, R., Chen, S., Peng, M., Klein, M., Geisler, M., Martinoia, E. (2003) Plant ABC Transporters. In: Book ABC transporters from bacteria to humans, SP Cole, K Kuchler, C Higgins, B Holland (eds), Academic Press, UK  pp.335-356

  Chen, S., Glawishnig, E., Jorgensen, K., Naur, P., Jorgensen, B., Olsen, C.E., Rasmussen, H.,  Pickett, J.A., Halkier, B.A. (2003) CYP79F1 and CYP79F2 have distinct functions in the biosynthesis of aliphatic glucosinolates in Arabidopsis. Plant Journal 33, 923-937.

  Petersen, B.L.,* Chen, S.,* Hansen, C., Halkier, B.A. (2002) Composition and content of glucosinolates in developing Arabidopsis thaliana. Planta  214, 562-571.

  Chen, S., Andereason, E. (2001) Update on glucosinolate metabolism and transport. Plant Physiology and Biochemistry 39, 743-758 (Cover).

  Chen, S., Petersen, B.L., Olsen, C.E., Shulz, A., Halkier, B.A. (2001) Glucosinolate uptake and long-distance transport in Arabidopsis thaliana. Plant Physiology 127, 194-201.

  Chen, S., Halkier, B.A. (2000) In vivo synthesis and purification of radioactive  p-hydroxybenzylglucosinolate in sinapis  alba. Phytochemical Analysis 11, 174-178.

  Wittstock, U.*, Chen, S.*, Halkier, B.A. (2000) Expression cloning of plasma membrane transporter proteins by screening for uptake of radiolabelled substrates. Journal of Experimental Botany 51,  955-960.

  Chen, S., Halkier, B.A. (2000) Characterization of glucosinolate transporter in       Brassica napus  leaf cells. Journal of Biological Chemistry 275, 22955-22960.

  Chen, S., Schopfer, P. (1999) Hydroxyl radical production in physiological reactions - a novel function of peroxidase. European Journal of Biochemistry 260, 726-735.

  Chen, S., Halkier, B.A. (1999) Functional Expression and Characterization of Brassica  napus Myr1 myrosinase in Saccharomyces cerevisiae. Protein Expression and Purification17, 414-420.

  Chen, S., Li, L., Jiao, X.Z. (1998) Effect of osmotic shock on protein phosphoryl-ation in Dunaliella salina cells. Journal of Integrative Plant Biology 40, 126-131.

  Chen, S., Li, L., Yen, C.C., Xu, Z.K., Jiao, X.Z. (1997) Inositol phospholipid signal transduction system in Dunaliella salina  and its function in osmotic shock. Chinese Science 42, 151-155.

  Chen, S., Li, L., Yen, C.C., Jiao, X.Z. (1996) Relationship of plasmalemma redox activity to K+  uptake by Dunaliella salina cells. Journal of Integrative Plant Biology 38, 295-301.

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