Sixue Chen

Professor & Director of Proteomics Facility

Ph.D. Shanghai Institute of Plant Physiology & East China Normal University, 1996

438 Cancer & Genetics Research Complex
(352) 273-8330

schen@ufl.edu

Research Interests

My research is focused on the signaling and metabolic mechanisms underlying plant interaction with the environment. My lab research has been particularly focused on three topics: glucosinolate metabolism, guard cell signal transduction, and plant pathogen interaction.

Project 1. Glucosinolate metabolism. Glucosinolates are a group of naturally occurring thioglucosides, present in Brassica plants (e.g., canola and cabbage). Glucosinolate degradation products display diverse biological activities, including defense against 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 metabolites such as isothiocyanates exhibit anticarcinogenic properties. The core glucosinolate pathway has been well studied in Arabidopsis. However, we know little about how the components in different pathways interact to produce plant phenotypes and traits. Nor do we know how different layers of molecular control work together. The lack of such fundamental knowledge is a major reason why plant genetic engineering has been largely unsuccessful. It poses a chronic problem for rational engineering of crops for better quality and defense. Research in this project is focused on characterizing the regulatory and metabolic networks involving glucosinolate metabolism using multidisciplinary approaches. We aim to identify protein and metabolite changes in response to perturbation of glucosinolate metabolism and to integrate the data into glucosinolate networks. The process of networking will generate new testable hypotheses concerning glucosinolate metabolic pathways and related pathways. The ultimate objective is to use the immense biosynthetic potential of plants as an efficient, environmentally friendly and renewable source of fine chemicals and pharmaceuticals.

Project 2. Guard cell signaling networks. Guard cells are highly specialized plant epidermal cells that enclose tiny pores called stomata. Stomatal movements control both uptake of carbon dioxide and loss of water, and thus play important roles in plant growth and acclimation to environmental stresses. The plant hormone abscisic acid (ABA) is a key indicator of drought stress. ABA induces stomatal closure via an intricate intracellular signaling network in guard cells, thereby promoting plant water conservation. It is our central hypothesis that protein redox modification and dynamic changes in key metabolites are critical regulatory mechanisms in ABA signaling. We are testing the hypothesis by pursuing: identification of guard cell proteins whose redox status is altered in response to ABA and determination of their specific redox-sensitive amino acid residues, quantification of ABA-induced changes in metabolites implicated in guard cell signaling, and integration of the new information into a dynamic model of ABA-induced stomatal closure. Accomplishing these objectives is significant because it will reveal novel components of ABA signaling networks and provide knowledge of regulatory mechanisms underlying stomatal movements that will help to develop crops with enhanced stress tolerance and productivity.

Project 3. Plant pathogen interaction. The study of pathogen response and defense in crop species is of essential importance as the applications are directly related to agricultural production. Pseudomonas syringae pv tomato (Pst DC3000) causes speck disease in tomato (Solanum Lycopersicum), a crop growing in large quantities in Florida and having both nutritional and economical value. The goal of this project is to take what is known about pathogen host interactions and observe in greater detail mechanisms that plants utilize in response to pathogen infection at the posttranscriptional levels, including protein expression, redox and phosphorylation/dephosphorylation switches. Understanding changes in protein expression as well as redox and phospho-switches will provide important insights into how plant response and resistance to pathogens are occurring. Further investigation into unique/novel proteins and regulations will advance our knowledge of plant defense against pathogens, and allow researchers to use biotechnology to prevent future bacterial speck disease outbreaks.

Interestingly, as we gain more and more knowledge, the above projects have become interconnected with each other. Glucosinolate metabolism plays a role in pathogen defense and affects stomatal movement, which serves as the first line of defense against pathogen invasion. In addition to hypothesis generation projects, another major part of my research program has been hypothesis driven, i.e., characterizing molecular, biochemical and physiological functions of specific genes and proteins identified by proteomics and metabolomics approaches. One of the projects has been focused on understanding the key steps in the methionine chain-elongation pathway, which directly connects methionine (primary) metabolism to glucosinolate (spealized) metabolism. Our integration of hypothesis generation and hypothesis driven research will ultimately lead to a holistic view of cellular networks and processes in plants and will create important stepping stones towards potential biotechnological applications in enhanced yield, bioenergy and defense.

Publications

Zhu, M., Zhang, T., Ji, W., Geng, S., Silva-Sanchez, C., Song, W., Assmann, S.M., Harmon, A., Chen, S. (2016) Redox regulation of a stress hormone-activated serine/threonine protein kinase of Brassica napus. Journal of Experimental Botany (submitted).

Geng, S., Misra, B.B., de Armas, E., Huhman, D.V., Alborn, H.T., Sumner, L.W., Chen, S. (2016) Jasmonate-mediated stomatal closure under elevated CO2 revealed by time-resolved metabolomics. The Plant Journal doi: 10.1111/tpj.13296.

Misra, B.B.§ Yin, Z., Geng, S., Armas, E.D., Chen, S. (2016) Metabolomic responses of Arabidopsis suspension cells to bicarbonate under light and dark conditions. Scientific Reports (in press).

Lawrence, S. II, Parker, J., Chen, S (2016) Plant response to bacterial pathogens: A proteomics view. Agricultural Proteomics (G.H. Salekdeh ed.) 2, 203-225.

Libault, M., Chen, S., eds. (2016) E-Book: Plant Single Cell Type Systems Biology. Lausanne: Frontiers Media. doi: 10.3389/978-2-88919-948-8.

Libault, M., Chen, S. (2016) Plant single cell type systems biology. Frontiers in Plant Science 7:35. doi: 10.3389/fpls.2016.00035.

Zhang, T., Schneider, J.D., Zhu, N., Chen, S. (2016) Identification of MAPK substrates using quantitative phosphoproteomics. Methods in Molecular Biology (volume on “Plant Pattern Recognition Receptors”) (in press)

Mostafa, I., Zhu, N., Yoo, M.J., Balmant, K.M., Misra, B.B., Dufresne, C., Abou-Hashem, M., Chen, S., El-Domiaty, M. (2016) New nodes and edges in the glucosinolate molecular network revealed by proteomics and metabolomics of Arabidopsis myb28/29 and cyp79B2/B3. Journal of Proteomics 138, 1-19. doi: 10.1016/j.jprot.2016.02.012 (corresponding author).

Yoo, M-J., Ma, T., Zhu, N., Liu, L., Harmon, A.C., Wang, Q., Chen, S. (2016) Genome-wide identification and expression analysis of the SnRK2 genes in Brassica napus guard cells. Plant Molecular Biology 91(1), 211-227.

Misra, B.B., Armas, E.D., Chen, S. (2016) Differential metabolomic responses of PAMP-triggered immunity and effector-triggered immunity in Arabidopsis suspension cells. Metabolomics 12 (4), 1-15 doi: 10.1007/s11306-016-0984-y.

Zhang, T., Zhu, M., Zhu, N., Strul, J.M., Dufresne, C., Harmon, A.C., Chen, S. (2016) Identification of thioredoxin targets in guard cell enriched epidermal peels using cysTMT proteomics. Journal of Proteomics 133, 48-53 doi: 10.1016/j.jprot.2015.12.008.

Zhu, M., Jeon, B.W., Geng, S., Yu, Y., Balmant, K., Chen, S., Assmann, S.M. (2016) Preparation of epidermal peels and guard cell protopalsts for cellular, electrophysiological, and –omics assays of guard cell function. Methods in Molecular Biology 1363, 89-121 (doi: 10.1007/978-1-4939-3115-6_9).

Balmant, K., Zhang, T., Chen, S. (2016) Protein phosphorylation and redox modification in stomatal guard cells. Frontiers in Physiology 7:26. doi: 10.3389/fphys.2016.00026.

Zhou, X., Andrade, M.O., Teper, D., Zhang, T., Chen, S., Song, W., Wang, N. (2016) A phosphorylation switch on Lon protease determines the fate of bacterial type III secretion system in host” (reference number: NMICROBIOL-16071034), Nature Microbiology

Li, H., Wang, Y., Ma, C., Gu, D., Nan, J., Chen, S. (2016) Overexpression of S-adenosyl-L-methionine synthetase2 from Sugar beet M14 increased Arabidopsis tolerance to salt and oxidative stress. Plant and Soil (submitted)

Klee, S., Mostafa, I., Chen, S., Dufresne, C., Lehman, B.L., Sinn, J.P., Peter, K.A., McNellisa, T.W. (2016) An Erwinia amylovora yjeK mutant has numerous environmentally-dependent phenotypic and proteomic alterations. Journal of Bacteriology (submitted)

Suo, J., Zhang, H., Zhao, Q., Song, B., Cao, J., Chen, S., Wang, T., Luo, J., Guo, L., Zhang, X., Ma, J., She, Y., Dai, S. (2016) Na2CO3-responsive photosynthetic and ROS scavenging mechanisms in chloroplasts of halophyte Puccinellia tenuiflora revealed by proteomics and phosphoproteomics. New Phytologist (submitted)

Liu, L., Liu, H., Li, S., Zhang, X., Zhang, M., Zhu, N., Dufresne, C.P., Chen, S., Wang, Q. (2016) Regulation of BZR1 in fruit ripening revealed by iTRAQ proteomics analysis. Nature Scientific Reports (in press).

Feng, B., Ma, S., Chen, S., Zhu, N., Zhang, S., Yu, B., Yu, Y., Chen, X., Dinesh-Kumar, S.P., Shan, L., He, P. (2016) Proteome-wide identification of protein poly(ADP-ribosyl)ation targets reveals an important role of DAWDLE in Arabidopsis immunity. The EMBO Journal (in press).

Zhang, M., Koh, J., Liu, L., Shao, Z., Zhu, N., Dufresne, C.P., Chen, S., Wang, Q. (2016) Critical role of SlCOI1 dependent jasmonate pathway in AAL toxin induced PCD revealed by comparative proteomics. Scientific Reports 6, 28451 doi: 10.1038/srep28451.

Wang, J., Yu, Q., Xiong, H., Wang, J., Chen, S., Yang, Z., Dai, S. (2016) Proteomic insight into the response of Arabidopsis chloroplasts to darkness. Plos One (in press)

Ji, W., Li, S., Cong, R., Li, R., Qin, Z., Li, Y., Zhou, X., Chen, S., Li, J. (2016) Quantitative proteomics analysis 1 of soybean leaves and roots during the initial stage of salt stress. Frontiers in Plant Science (in press)

Yu, J., Guo, H., Zhang, J., Zhao, Q., Liu, Y., Chen, S., Shi, L., Dai, S. (2016) The leaf color regulation mechanism in Chimera Hosta ‘Gold standard’ leaves revealed from proteomic analysis. International Journal of Molecular Sciences (in press)

Meng, X., Zhao, Q., Jin, Y., Yu, J., Yin, Z., Chen, S., Dai, S. (2016) Chilling-responsive mechanisms in halophyte Puccinellia tenuiflora seedlings revealed from proteomics analysis. Journal of Proteomics (in press, http://dx.doi.org/10.1016/j.jprot.2016.04.038).

Soltis, D., Misra, B.B., Shan, S., Chen, S., Soltis, P. (2016) Polyploidy and the proteome. BBA – Proteins and Proteomics (in press).

Goncalves, E., Koh, J., Zhu, N., Yoo, M-J., Chen, S., Matsuo, T., Rathiansabapathi, B. (2016) Nitrogen starvation-induced triacylglycerol accumulation in the green algae: Evidence for regulation by ROC40, a transcription factor known in circadian rhythm. The Plant Journal (in press).

Ji, W., Koh, J., Li, S., Zhu, N., Dufresne, C.P., Zhao, X., Chen, S., Li, J. (2016) Quantitative proteomics reveals an important role of GsCBRLK in salt stress response of soybean. Plant and Soil (in press).

Wu, Y., Hepowit, N., Dantuluti, S., Chen, H., Chen, S., Maupin-Furlow, J. (2016) Proteome targets of ubiquitin-like samp1ylation are associated with sulfur metabolism and oxidative stress in Haloferax volcanii. Proteomics (in press, doi: 10.1002/pmic.201500153).

Lazensky, R., Silva-Sanchez, C., Li, J., Chow, M., Chen, S., Kroll, K.J., Tripp, K., Walsh, M., Denslow, N. (2016) Investigating an increase in Florida Manatee (Trichechus Manatus Latirostris) mortalities in 2013 using a proteomic approach. The Marine Mammal Science Journal (submitted)

Zhao, Q., Suo, J., Chen, S., Jin, Y., Ma, X., Yin, Z., Zhang, Y., Wang, T., Luo, J., Jin, W., Zhou, Z., Dai, S. (2016) Na2CO3-responsive mechanisms in halophyte Puccinellia tenuiflora roots revealed by physiological and proteomic analyses. Nature Scientific Reports 111.

Fu, X., Liu, R., Sanchez, I., Silva-Sanchez, C., Hepowit, N.L., Cao, S., Chen, S., Maupin-Furlow, J. (2016) Ubiquitin-like proteasome system represents a eukaryotic-like pathway for targeted proteolysis in Archaea. mBio 7(2), e00379-16. (doi:10.1128/mBio.00379-16).

Law, M.E., Ferreira, R.B., Davis, B.J., Higgins, P.J., Kim, J.S.,  Castellano, R.K., Chen, S., Luesch, H., Law, B.K. (2016) CUB domain-containing protein 1 and the epidermal growth factor receptor cooperate to induce cell detachment. Breast Cancer Research (in press).

Misra, B.B., Armas, E.D., Tong, Z., Chen, S. (2015) Metabolomic responses of guard cells and mesophyll cells to bicarbonate. PLOS One 10(12), e0144206.

Zhang, T., Chen, S., Harmon, A.C. (2015) Protein-protein interactions in plant MAP kinase cascades. Journal of Experimental Botany 67(3), 607-618. doi: 10.1093/jxb/erv508.

Balmant, K.M., Parker, J., Zhu, N., Dufresne, C., Chen, S. (2015) Redox proteomics of tomato in response to Pseudomonas syringae infection. Horticulture Research 0, 15042; doi:10.1038/hortres.2015.43.

Misra, B.B., Acharya, B.R., Granot, D., Assmann, S.M., Chen, S. (2015) The guard cell metabolome: functions in stomatal movement and global food security. Frontiers in Plant Science 6, 334. doi: 10.3389/fpls.2015.00334.

Koh, J., Chen, G., Yoo, M., Zhu, N., Dufresne, D., Erickson, J.E., Shao, H., Chen, S. (2015) Comparative proteomic analysis of Brassica napus in response to drought stress. Journal of Proteome Research 14, 3068-3081. doi: 10.1021/pr501323d.

Misra, B.B., Chen, S. (2015) Advances in understanding CO2 responsive plant metabolomes in the era of climate change. Metabolomics 11, 1478-1491.

Zhang, T., Zhu, M., Song, W., Harmon, A., Chen, S. (2015) Oxidation and phosphorylation of MAP kinase 4 causes protein aggregation. BBA – Proteins and Proteomics 1854, 156-165 (doi:10.1016/j.bbapap.2014.11.006).

Parker, J., Balmant, K., Zhu, F., Zhu, N., Chen, S. (2015) cysTMTRAQ – An integrated proteomics method for identification of thiol-based redox proteins. Molecular and Cellular Proteomics 14, 237-242 (doi: 10.1074/mcp.O114.041772).

Zhang, Y.T., Zhang, Y.L., Chen, S., Yin, G.H., Yang, Z., Lee, S., Liu, C.G., Zhao, D.D., Ma, Y.K., Song, F.Q., Bennett, J.W., Yang, F.S. (2015) Proteomics of methyl jasmonate induced defense in maize leaves against Asian corn borer. BMC Genomics (in press, MS: 1817473372144616).

Zhang, C., Pang, Q., Xue, M., Long, J., Chen, S., He, Y. (2015) Dihydroxyacid dehydratase is crucial for gametophyte development and the disruption causes increased susceptibility to salinity stress in Arabidopsis. Journal of Experimental Botany 66, 879-888 (doi: 10.1093/jxb/eru449) (co-correspondence).

Silva-Sanchez, C., Li, H., Chen, S. (2015) Recent advances and challenges in plant phosphoproteomics. Proteomics 15, 1127-1141 (doi: 10.1002/pmic. 201400410).

Dai, S., Pang, Q., Tian, Y., Chen, S., Yan, X. (2015) Proteomic analysis of Arabidopsis leaves subjected to mechanical wounding. Current Proteomics 12, (in press, 13 printed pages).

Shao, H., Chen, S., Brestic, M. (2015) Environment-living organism’s interactions from physiology to genomics. Intl. J. Genomics 270736 (http://dx.doi.org/10.1155/2015/270736).

Zhao, Q., Suo, J., Gao, J., Wang, T., Chen, S., Dai, S. (2015) Cytological and proteomic analyses of horsetail (Equisetum arvense) spore germination. Frontiers in Plant Science 6, 441 (doi:10.3389/fpls.2015.00441).

Suo, J., Zhao, Q., Zhang, Z., Chen, S., Cao, J., Wei, X., Wang, T., Dai, S. (2015) Cytological and proteomic analyses of Osmunda cinnamomea L. var. asiatica spore germination. Molecular and Cellular Proteomcs 14(9), 2510-2534. doi: 10.1074/mcp.M114.047225.

Cahoon, R.E., Lutke, W.K., Cameron, J.C., Chen, S., Lee, S.G., Rivard, R.S., Rea, P.A., Jez, J. (2015) Counter-intuitive evolution of phytochelatin-based heavy metal tolerance. Journal of Biological Chemistry 290, 17321-17330 (pii: jbc.M115.652123).

Li, B., Jiang, S., Yu, X., Cheng, C., Chen, S., Chen, Y., Yuan, J.S., Jiang, D., He, P., Shan, L. (2015) Phosphorylation of a trihelix transcription repressor ASR3 by MPK4 negatively regulates Arabidopsis immunity. The Plant Cell 27, 839-856 (doi: 10.1105/tpc.114.134809).

Xue, M., Long, J., Jiang, Q., Wang, M., Chen, S., Pang, Q., He, Y. (2015) Distinct patterns of histone mark associated with recruitment of methionine chain-elongation pathway from leucine biosynthesis. Journal of Experimental Botany 66, 805-812 ( doi: 10.1093/jxb/eru440).

Li, H., Pan, Y., Zhang, Y., Wu, C., Ma, C., Yu, B., Zhu, N., Koh, J., Chen, S. (2015) Salt stress response of membrane proteome of sugar beet monosomic addition line M14. Journal of Proteomics 127, 18-33 (doi: 10.1016/j.jprot.2015.03.025).

Suo, J., Chen, S., Zhao, Q., Shi, L., Dai, S. (2015) Fern spore germination in response to environmental factors. Frontiers in Biology (in press) (doi:  10.1007/s11515-015-1342-6).

Li, J., Silva-Sanchez, C., Zhang, T., Chen, S., Li., H. (2015) Phosphoproteomics technologies and applications in plant biology research. Frontiers in Plant Science (in press).

Hu, G., Koh, J., Yoo, M.J., Chen, S., Wendel, J.F. (2015) Gene-expression novelty in allopolyploid cotton: a proteomic perspective. Genetics  200 (1), 91-104.

Eade, C., Diaz, C., Chen, S., Cole, A., Cole, A. (2015) HIV-enhancing factors are secreted by reproductive epithelia upon inoculation with bacterial vaginosis-associated bacteria. Protein and Peptide Letters 22(8), 672-680.

Zheng, T., Pierre-Pierre, N., Yan, X., Huo, Q., Almodovar, A., Valerio, F., Rivera-Ramirez, I., Griffith, E., Decker, D., Chen, S., Zhu, N. (2015) A gold nanoparticle-enabled blood test for early stage cancer detection and risk assessment. ACS Applied Materials and Interfaces 7, 6819-6827 (doi: 10.1021/acsami.5b00371).

Misra, B.B., Assmann, S.M., Chen, S. (2014) Plant single cell and single cell-type metabolomics. Trends in Plant Science 19, 637-646 (invited review).

Yan, H., Yoo, M.J., Koh, J., Liu, L., Chen, Y., Acikgoz, D., Wang, Q., Chen, S. (2014) Systems analysis of transcriptomic and metabolic reprograming of Arabidopsis in response to perturbation of jasmonate signaling. Journal of Proteome Research 13, 5751-5766.

Zhang, T., Chen, S., Harmon, A. (2014) Protein phosphorylation in stomatal movement. Plant Signaling & Behavior 9: 11, e972845 (doi: 10.4161/15592316.2014.972845).

Zhu, M., Zhu, N., Chen, Q., Song, W., Harmon, A., Assmann, S., Chen, S (2014) Thiol-based redox proteins in guard cell hormone signaling. The Plant Journal 78, 491-515.

Chen, S. (2014) Redox and phosphorylation regulated proteins in plant stomatal signaling. Journal of Proteins and Proteomics 5 (3), 65. (not peer-reviewed)

Li, F., Cheng, C., Cui, F., De Oliveira, M.V., Intorne, A.C., Babilonia, K., Li, M., Chen, S., Metz, R., Johnson, C.D.,  Koiwa, H., Sun, W., Li, Z., de Souza Filho, G., Shan, L., He, P (2014) Pathogen-induced phosphorylation relay on RNA polymerase II orchestrates plant immunity. Cell Host and Microbe 16, 748-758. doi: 10.1016/j.chom.2014.10.018.

Lin, W., Li, B., Chen, S., Zhu, N., He, P., Shan, L. (2014) Tyrosine phosphorylation of BAK1/BIK1 mediates Arabidopsis innate immunity. Proceedings of National Academy of Sciences 111, 3632-3637. doi: 10.1073/pnas.1318817111.

Yang, L., Fountain, J.C., Jiang, T., Scully, B.T., Lee, R.D., Kemerait, R.C., Chen, S., Guo, B. (2014) Protein profiles reveal diverse drought-responsive signaling pathways in maize kernels. International Journal of Molecular Sciences 15, 18892-18918.

Parka, Y-J., Koh, J., Gaunaa, A.E., Chen, S., Cha, S. (2014) Identification of regulatory factors for mesenchymal stem cell-derived salivary epithelial precursors. Plos One 9 (11), e112158.

Hu, G., Koh, J., Yoo, M.J., Pathak, D., Chen, S., Wendel, J.F. (2014) Cotton domestication and comparative evolutionary proteomics. Planta  40, 1237-1251.

Silva-Sanchez, C., Chen, S., Li, J., Chourey, P.S. (2014) A comparative glyco-proteome study of transfer cells-enriched basal endosperm in the hexose-deficient miniature1 (mn1) seed mutant and its wild type Mn1 in maize. Frontiers in Plant Science 5, 63. doi: 10.3389/fpls.2014.00063

Li, H., Chen, S. (2014) Protomics – Studies on the proteome of sugarbeet line M14. Chemical Industry Press, Beijing, China.

Jin, X., Wang, R., Zhu M, Jeon BW, Albert, R., Chen, S., Assmann, S. (2013) Abscisic acid-responsive guard cell metabolomes of Arabidopsis wild-type and gpa1 G-protein mutants. The Plant Cell 25, 4789-4811.

Agrawal, G.K., Job, D., Kieselbach, T., Barkla, B.J., Chen, S., Deswal, R., Amalraj, R.S., Cramer, R., Weckwerth, W., Wienkoop, S., Ndimba, B.K., Tanou, G., Luthje, S., Dunn, M.J., Kim, S.T., Fukao, Y., Yonekura, M., Zolla, L., Rohila, J.S., Waditee-Sirisattha, R., Masi, A., Wang, T., Sarkar, A., Agrawal, R., Renaut, J., Rakwal, R. (2013) INPPO actions and recognition as a driving force for progress in plant proteomics: change of guard, INPPO update, and upcoming activities. Proteomics 13, 3093-3100.

Keshavamurthy, R., Koh, J., Chen, S., Chalam, K.V. (2013) Quantitative proteomics of vitreous humor to identify potential markers involved in the induction of posterior vitreous detachment. Investigative Ophthalmology and Visual Science 54, 3306.

Liu, L., Jia, C., Zhang, M., Chen, D., Chen, S., Guo, R., Guo, D., Wang, Q. (2013) Ectopic expression of a BZR1-1D transcription factor in brassinosteroid signalling enhances carotenoid accumulation and fruit quality attributes in tomato. Plant Biotechnology Journal 1-11, doi: 10.1111/pbi.12121.

Yang, L., Zhang, Y., Zhu, N., Koh, J., Ma, C., Pan, Y., Yu, B., Li, H., Chen, S. (2013) Proteomic analysis of salt tolerance in Sugar beet monosomic addition line M14. Journal of Proteome Research 12, 4931-4950.

Torrazza, R.M., Li, N., Young, C., Kobeissy, F., Chow, M., Chen, S., Mai, V., Sharma, R., Hudak, M., Shuster, J., Neu, J. (2013) Pilot study using proteomics to identify predictive biomarkers of necrotizing enterocolitis from buccal swabs in very low birth weight infants. Neonatology 104, 234-242.

Chen, Y., Fei, M., Wang, Y., Chen, S., Yan, X. (2013) Proteomic investigation of systemic glucosinolate changes in Arabidopsis rosette leaves to exogenous methyl jasmonate. Plant Biosystems DOI: 10.1080/11263504.2013.819044.

Silva-Sanchez, C., Chen, S., Zhu, N., Li, Q.B., Chourey, P.S. (2013) Proteomic comparison of basal endosperm in Maize miniature1 mutant and its wild-type Mn1. Frontiers in Plant Physiology 4, 211. doi: 10.3389/fpls.2013.00211.

Hu, G., Koh, J., Yoo, M.J., Grupp, K., Chen, S., Wendel, J.F. (2013) Proteomic profiling of developing cotton fibers from wild and domesticated Gossypium barbadense. New Phytologist 200, 570-582.

Tan, L., Chen, S., Wang, T., Dai, S. (2013) Proteomic insights into seed germination in response to environmental factors. Proteomics 13, 1850-1870.

Gray, J.W., Dittrich, A.C.N., Chen, S., Avila, J., Giavalisco, P., Devarenne, T. (2013) Two Pdk1 phosphorylation sites on the plant cell death suppressor Adi3 contribute to substrate phosphorylation. BBA – Proteins and Proteomics 1834, 1099-1106.

Zhao, Q., Zhang, H., Wang, T., Chen, S., Dai, S. (2013) Proteomics-based investigation of salt-responsive mechanisms in plant roots. Journal of Proteomics 82, 230-253.

Yu, J., Chen, S., Wang, T., Sun, G., Dai, S. (2013) Comparative proteomic analysis of Puccinellia tenuiflora leaves under Na2CO3 stress. International Journal of Molecular Sciences 14, 1740-1762.

Parker, J., Koh, J., Yoo, M., Zhu, N., Feole, M., Yi, S., Chen, S. (2013) Quantitative proteomics of tomato defense against Pseudomonas syringae infection. Proteomics 13, 1934-1946.

Zhao, Q., Chen, S., Dai, S. (2013) C4 photosynthetic machinery: insights from maize chloroplast proteomics. Frontiers in Plant Science 4 (85), 1-6. doi: 10.3389/fpls.2013.00085.

Li, H., Ji, L., Ma, C., Wang, B., Liu, Y., Yu, B., Chen, S. (2013) Molecular cloning and characterization of a rat sarcoma-like protein from brain (Rab) gene in sugar beet monosomic additional line M14. Australian Journal of Crop Science 7, 374-380.

Wu, C., Ma, C., Pan, Y., Gong, S., Zhao, C., Chen, S., Li, H. (2013) Sugar beet M14 glyoxalase I gene can enhance plant tolerance to abiotic stresses. Journal of Plant Research 126, 415-425.

Chen, S. (2012) Proteomic characterization of stomatal movement. Plant Science J. 30 (sup.), 12.

Gao, X., Chen, X., Lin, W., Chen, S., Lu, D., Niu, Y., Li, L., Cheng, C., McCormack, M., Sheen, J., Shan, L., He, P. (2012) Bifurcation of Arabidopsis NLR immune signaling via Ca2+-dependent protein kinases. PLOS Pathogens 9(1): e1003127. doi:10.1371/journal.ppat.1003127.

He, Y., Dai, S., Dufresne, C.P., Zhu, N., Pang, Q., Chen, S. (2012) Integrated proteomics and metabolomics of Arabidopsis acclimation to gene-dosage dependent perturbation of isopropylmalate dehydrogenases. PLOS ONE 8(3): e57118. doi:10.1371/journal.pone.0057118.

You, J., Lee, E., Bonilla, L., Francis, J., Koh, J., Block, J., Chen, S., Hansen, P.J. (2012) Treatment with the proteasome inhibitor MG132 during the end of oocyte maturation improves oocyte competence for development after fertilization in cattle. PLOS One 7(11): e48613. doi:10.1371/journal.pone.0048613.

Hepowit, N., Uthandi, S., Miranda, H.V., Toniutti, M.,  Olivarez, O.,  De Vera, S.M.S., Fanucci, G.E., Chen, S., Maupin-Furlow, J.A. (2012) Archaeal JAB1/MPN/MOV34 metalloenzyme (HvJAMM1) cleaves ubiquitin-like small archaeal modifier proteins (SAMPs) from protein-conjugates. Molecular Microbiology 86, 971-987.

Zhu, M., Dai, S., Zhu, N., Booy, A., Simons, B., Yi, S., Chen, S. (2012) Methyl jasmonate responsive proteins in Brassica napus guard cells revealed by iTRAQ based quantitative proteomics. Journal of Proteome Research 11, 3728-3742.

 Avila, J., Gregory, O.G., Su, D., Deeter, T.A., Chen, S., Silva-Sanchez, C., Xu, S.,  Martin, G.B., Devarenne, T.P. (2012) The β-subunit of the SnRK1 complex is phosphorylated by the plant cell death suppressor Adi3. Plant Physiology 159, 1277-1290.

Koh, J., Chen, S., Zhu, N., Yu, F., Soltis, P.S., Soltis, D.E. (2012) Comparative proteomics of the recently and recurrently formed natural allopolyploid Tragopogon mirus (Asteraceae) and its parents. New Phytologist 196, 292-305.

Wang, Y., Ma, C., Wu, C., Gong, S., Chen, S., Li, H (2012) Cloning of a cystatin gene from sugar beet M14 that can enhance salt and drought tolerance of Arabidopsis seedlings. Plant Science 191-192, 93-99.

Dai, S., Chen, S. (2012) Single-cell-type proteomics toward a holistic understanding of plant functions. Molecular and Cellular Proteomics 11, 1-9 (invited review).

Law, L.E., Corsino, P.E., Jahn, S.C., Davis, B.J., Chen, S., Patel, B., Pham, K., Lu, J., Sheppard, B., Nørgaard, P., Hong, J., Luesch, H., Law, B.J. (2012) Glucocorticoids and histone deacetylase inhibitors cooperate to block the invasiveness of basal-like breast cancer cells through novel mechanisms. Oncogene 1-14.

Yang, L., Ma, C., Wang, L., Chen, S., Li, H. (2012) Salt stress induced proteome and transcriptome changes in sugar beet monosomic addition line M14. Journal of Plant Physiology 169, 839-850.

Dai, S., Chen, S. (2012) Information processing at the proteomics level. Springer Handbook of Bio- and Neuroinformatics (HBBNI), edited by Prof. Nikola Kasabov (Chapter 4, in press).

Zhu, N., Zhu, M.M., Dai, S., Zheng, R., Chen, S. (2012) Development of an improved isotope-coded affinity tag technology for thiol redox proteomics. Journal of Integrated-OMICS 2, 17-23.

Pang, Q., Guo, J., Chen, S., Chen, Y., Zhang L., Fei, M., Jin, S., Li, M., Wang, Y., Yan, X. (2012) Effect of salt treatment on the glucosinolate-myrosinase system in Thellungiella salsuginea. Plant Soil 355, 363-374.

Chen, Y., Pang, Q., He, Y., Zhu, N., Branstrom, I., Yan, X., Chen, S. (2012) Proteomics and metabolomics of Arabidopsis responses to perturbation of glucosinolate biosynthesis. Molecular Plant 5, 1138-1150.

Zhu, M., Dai, S., Chen, S. (2012) The stomata frontline of plant interaction with the environment-perspectives from hormone regulation. Frontiers in Biology 7, 96-112.

Benskin, J., Chen, S. (2012) Proteomics in the classroom: an investigative study of proteins in microorganisms. The American Biology Teacher 74, 237–243.

Parker, J., Zhu, N., Zhu, M., Chen, S. (2012) Profiling thiol redox proteome using isotope tagging mass spectrometry. Journal of Visual Experiments 61, e3766 (doi:10.3791/3766).

Agrawal, G.K., Sarkar, A., Agrawal, R., Ndimba, B.K., Tanou, G., Dunn, M.J., Kieselbach, T., Cramer, R., Wienkoop, S., Chen, S., Rafudeen, M.S., Deswal, R., Barkla, B.J., Weckwerth, W., Heazlewood, J.L., Renaut, J., Job, D., Rakwal, R. (2012) Boosting the globalization of plant proteomics through INPPO: current developments and future prospects. Proteomics 12, 359-368.

Zhang, H., Han, B., Wang, T., Chen, S., Li, H., Zhang, Y., Dai, S. (2012) Mechanisms of plant salt response: insights from proteomics. Journal of Proteome Research 11, 49-67.

Yu, J., Chen, S., Zhao, Q., Wang, T., Yang, C., Diaz, C. , Sun, G., Dai, S. (2011) Physiological and proteomic analysis of salinity tolerance in Puccinellia tenuiflora. Journal of Proteome Research 10, 3852-3870.

He, Y., Galant, A., Pang, Q., Strul, J.M., Balogun, S.F., Jez, J.M., Chen, S. (2011) Structural and functional evolution of isopropylmalate dehydrogenases in leucine and glucosinolate pathways of Arabidopsis thaliana. Journal of Biological Chemistry 286, 28794-28801.

Ma, C., Wang, Y., Wang, Y.T., Wang, L., Chen, S., Li, H. (2011) Identification of a sugar beet BvM14-MADS box gene through differential gene expression analysis of monosomic addition line M14. Journal of Plant Physiology 168, 1980-1986.

Muthukrishnan, G., Quinn, G.A., Lamers, R.P., Diaz, C., Cole, A.L., Chen, S., Cole, A.M. (2011) Exoproteome of Staphylococcus aureus reveals putative determinants of nasal carriage. Journal of Proteome Research 10, 2064-2078.

Knoll, J.E., Ramos, M.L., Zeng, Y., Holbrook, C., Chow, C., Chen, S., Maleki, S., Bhattacharya, A., Ozias-Akins, P. (2011) TILLING for allergen reduction and improvement of quality traits in peanut (Arachis hypogaea L.). BMC Plant Biology 11, 81 (doi:10.1186/1471-2229-11-81).

Chen, Y., Pang, Q., Dai, S., Wang, Y., Chen, S., Yan, X. (2011) Proteomic identification of differentially expressed proteins in Arabidopsis in response to methyl jasmonate. Journal of Plant Physiology 168, 995-1008.

Chen, Y., Yan, X., Chen, S. (2011) Bioinformatic analysis of molecular network of glucosinolate biosynthesis. Computational Biology and Chemistry 35, 10-18.

He, Y., Chen, L., Zhou, Y., Mawhinney, T.P., Chen, B., Kang, B-H., Hauser, B.A., Chen, S. (2011) Functional characterization of Arabidopsis isopropylmalate dehydrogenases reveals their important roles in gametophyte development. New Phytologist 189, 160-175.

Wang, X., Chen, S., Zhang, H., Shi, L., Cao, F., Guo, L., Xie, Y., Wang, T., Yan, X., Dai, S. (2010) Desiccation tolerance mechanism in resurrection fern-ally Selaginella tamariscina revealed by physiological and proteomic analysis. Journal of Proteome Research 9, 6561-6577.

He, Y., Chen, B., Pang, Q., Strul J.M., Chen, S. (2010) Functional specification of Arabidopsis isopropylmalate isomerases in glucosinolate and leucine biosynthesis. Plant and Cell Physiology 51, 1480-1487.

Wang, Y., Li, H., Chen, S. (2010) Advances in quantitative proteomics. Frontiers in Biology 5, 195-203.

Han, B., Chen, S., Dai, S§., Yang, N., Wang, T. (2010) iTRAQ-based comparative proteomics reveals the features of plasma membrane-associated proteomes of pollen grains and pollen tubes from Lilium davidii Duch. Journal of Integrative Plant Biology 52, 1043-1058.

Pang, Q., Chen, S., Dai, S., Chen, Y., Wang, Y., Yan, X. (2010) Comparative proteomics of salt tolerance in Arabidopsis thaliana and Thellungiella halophila. Journal of Proteomics Research 9, 2584-2599.

Kang, S., Chen, S., Dai, S. (2010) Proteomics characteristics of rice leaves in response to environmental factors. Frontiers in Biology 5, 246-254 (cover).

Humbard, M.A., Miranda, H.V., Lim, J.M, Krause, D.J., Pritz, J.R., Zhou, G., Chen, S., Wells, L., Maupin-Furlow, J.A. (2010) Ubiquitin-like Small Archaeal Modifier Proteins (SAMPs) and their conjugation to proteins in Haloferax volcanii. Nature 463, 54-60.

Zhu, M., Simons, B., Ning, Zhu., Oppenheimer, D.G., Chen, S. (2010) Analysis of abscisic acid responsive proteins in Brassica napus guard cells by multiplexed isobaric tagging. Journal of Proteomics 73, 790-805.

Zhang, X., Chen, S., Mou, Z. (2010) Nuclear localization of NPR1 is required for regulation of salicylate tolerance, isochorismate synthase1 expression and salicylate accumulation in Arabidopsis. Journal of Plant Physiology 167, 144-148.

Li, H., Cao, H., Wang, Y., Pang, Q.Y., Ma, C., Chen, S. (2009) Proteomic analysis of sugar beet apomictic monosomic addition line M14. Journal of Proteomics73, 297-308.

He, Y., Mawhinney, T.P., Preuss, M.L., Schroeder, A.C., Chen, B., Abraham, L., Jez, J.M., Chen, S. (2009) A redox active isopropylmalate dehydrogenase functions in the biosynthesis of glucosinolates and leucine in Arabidopsis. Plant Journal 60, 679-690.

Alvarez, S., Zhu, M., Chen, S. (2009) Proteomics of Arabidopsis redox proteins in response to methyl jasmonate. Journal of Proteomics 73, 30-40.

Zhu, M., Dai, S., McClung, S., Yan, X., Chen, S. (2009) Functional differentiation of Brassica napus guard cells and mesophyll cells revealed by comparative proteomics. Molecular and Cellular Proteomics 8, 752 – 766 (cover).

Raichaudhuri, A., Peng, M., Naponelli, V., Chen, S., Sánchez-Fernández, R., Gu, H., Gregory III, J.F., Hanson, A.D., Rea, P.A. (2009) Plant vacuolar ABA transporters that translocate folates and antifolates in vitro and confer antifolate tolerance in vivo. Journal of Biological Chemistry 284, 8449 – 8460.
Pang, Q.Y., Chen, S., Li, L., Yan, X. (2009) Characterization of glucosinolate-myrosinase system in developing salt cress Thellungiella halophila. Physiologia Plantarum 136, 1-9.

Low, J.M., Chauhan, A.K., Gibson, D.S., Zhu, M., Chen, S., Rooney, M.E., Moore, T.L. (2009) Proteomic analysis of circulating immune complexes in juvenile idiopathic arthritis reveals disease-associated proteins. Proteomics-clinical applications 3, 829-840.

Paul, A.L., Liu, L., McClung, S., Laughner, B., Chen, S., Ferl, R.J. (2009) Comparative interactomics: analysis of arabidopsis in vivo 14-3-3 complexes reveals highly conserved 14-3-3 interactions between humans and plants. Journal of Proteome Research 8, 1913-1924.

Alvarez, S., Wilson, G.H., Chen, S. (2009) Proteomic analysis of in vivo redox regulated proteins in Arabidopsis. Journal of Chromatography B 877, 101-104.

Chen, Y., Chen S., Yan, X. (2008) Effect of environment on glucosinolate metabolism in plant. Acta Ecologica Sinica 28, 2829-2834.

Alvarez, S., He, Y., Chen, S. (2008) Comparative investigations of glucosinolate-myrosinase system in Arabidopsis suspension cells and hypocotyls. Plant Cell and Physiology 49, 324-333.

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.

Chen, S., Yen, C.C., Jiao, X.Z. (1996) Effect of osmotic shock on the redox system in the plasma membrane of Dunaliella salina. Cell Research 1996, 6, 31-38.

Current Graduate Students

Name
Email
Research Interest
Kelly Balmant balmant@ufl.edu Guard cell signaling
Sisi Geng sisigeng@ufl.edu Guard cell metabolomics
Sheldon Lawrence s.lawrence@ufl.edu Guard cell redox signaling
Joe Collins jcoll86@ufl.edu Proteomics of gene transcriptional control
Lisa David lisaidavid@ufl.edu Stomatal immunity proteomics
Tianyi Ma tyma@ufl.edu Guard cell kinases
Wenwen Kong wenwendadi@ufl.edu Glucosinolate metabolism and CAM

 

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