Systems and Synthetic Biology Cluster, Chair
Plant Metabolic Engineering
Redirecting carbon metabolism to increase yield
Camelina sativa is an excellent oil crop for biofuel production because it grows with little water and fertilizer on marginal land. To improve camelina as a dedicated biofuel plant, we have increased its photosynthetic CO2-fixation rates by modifying CO2 transport, assimilation and allocation and reducing the cost of photorespiraton. To extend its agricultural range, we are improving its stress tolerance against heat and drought. We are currently working on new technologies to modify the plastid genome and introduce a synthetic, RUBISCO-independent CO2 fixation cycle.
Marine microalgae and cyanobacteria
We are focussing on the marine microalgae as a feedstock for bioenergy and as a platform for the production of industrial enzymes or biopharmaceuticals. Our group is developing tools for transformation of algae. We are using several different approaches to optimize lipid and fatty acid production through genetic engineering of metabolic pathways and flux. To identify endogenous regulators of lipid metabolism in Dunaliella, we are analyzing differential gene expression by nextgen sequencing of Dunaliella cultures grown under environmental conditions that modify lipid profiles.
Genomic networks of abiotic stress responses in roots.
Plant root growth and development is a major factor in the adaptation of plants to site, in the establishment of the architecture of the whole plant, and in the plant’s ability to take up, transport and sequester water and nutrients. The direction of primary root growth is guided by the vector of gravity and the plants ability to sense mechanical stress, light quality and direction, and nutrient availability. We have identified the transcriptional networks integrating the response of roots to changes in their orientation (gravity) and mechanical impedance. High-throughput mutant screens, pyrosequencing, cell biology, and microarray technology enabled us to identify key regulators of signaling pathways. We are currently using systems approaches and bioinformatics algorithms to characterize the integration of different directional stimuli into a single growth response on a cellular level. Many of the key factors are themselves regulated by miRNA and siRNA species, which led us to sequencing the entire sRNA population in Arabidopsis roots. We identified many novel sRNAs and miRNAs and are currently characterizing their function in post-transcriptional and translational control. This research has been funded by NASA and utilized the International Space Station (ISS) and the Space Shuttle for the analysis of plant growth under microgravity.
Dalal, J., Lewis, D.R., Tietz, O., Brown, E.M., Brown, C.S., Palme, K., Muday, G.K. and Sederoff, H.W., 2016. ROSY1, a novel regulator of gravitropic response is a stigmasterol binding protein. Journal of Plant Physiology, 196, pp.28-40. pmb.cals.ncsu.edu/…5/02/Rosy-JPP-2016.pdf
Dalal, J., Lopez, H., Vasani, N.B., Hu, Z., Swift, J.E., Yalamanchili, R., Dvora, M., Lin, X., Xie, D., Qu, R. and Sederoff, H.W., 2015. A photorespiratory bypass increases plant growth and seed yield in biofuel crop Camelina sativa. Biotechnology for biofuels, 8(1), p.1.
Delaux, Pierre-Marc, Guru V. Radhakrishnan, Dhileepkumar Jayaraman, Jitender Cheema, Mathilde Malbreil, Jeremy D. Volkening, Hiroyuki Sekimoto, Heike Sederoff et al. “Algal ancestor of land plants was preadapted for symbiosis.”Proceedings of the National Academy of Sciences (2015): 201515426, in print.
Dalal, Jyoti, Roopa Yalamanchili, Christophe La Hovary, Mikyoung Ji, Maria Rodriguez-Welsh, Denise Aslett, Sowmya Ganapathy, Amy Grunden, Heike Sederoff, and Rongda Qu. “A novel gateway-compatible binary vector series (PC-GW) for flexible cloning of multiple genes for genetic transformation of plants.” Plasmid 81 (2015): 55-62.
Dalal, J., Land, E., Vasani, N., He, L., Smith, C., Rodriguez-Welsh, M., Perera, I., and Sederoff, H. (2015) Methods for RNA Profiling of Gravi-responding Plant Tissues. In: Plant Gravitropism: Methods and Protocols; Methods in Molecular Biology (ed. Elison Blancaflor) 1309, 91-117.
Srirangan, S., Sauer,M.-L.,Howard, B., Dvora, M., Dums, J., Backman, P., Sederoff, H., (2015) Interaction of temperature and photoperiod increases growth and oil content in the marine microalgae Dunaliella viridis. PLoS ONE 10(5): e0127562. doi:10.1371/journal.pone.0127562
Howard, B.E.; Hu, Q., Babaoglu, A.C., Chandra, M., Borghi, M.,Tan, X.; He, L.,Winter Sederoff, H., Gassmann, W., Veronese, P., Heber, S. (2013) High-Throughput RNA Sequencing of Pseudomonas-Infected Arabidopsis Reveals Hidden Transcriptome Complexity and Novel Splice Variants. PLoS ONE, (8), 10. e74183
Wang, W.-C., Allen, E.,Campos, A.E., Killens Cade, R.,Dean, L.,Dvora, M., Jeremy G. Immer, J.G.,Mixson, S.,Srirangan, S., Sauer, M.-L., Schreck, S., Sun, K., Thapaliya, N.,Wilson, C., Burkholder, J., Grunden, A.M., Lamb, H.H., Sederoff, H., Stikeleather, L.F., Roberts, W.F. (2013) ASI: Dunaliella Marine Microalgae to Drop-In Replacement Liquid Transportation Fuel. Environmental Progress & Sustainable Energy 32 (4), 916-925.
Rueschhoff EE, Gillikin JW, Sederoff HW, Daub ME (2013) The SOS4 pyridoxal kinase is required for maintenance of vitamin B6-mediated process in chloroplasts. Plant Physiology and Biochemistry; 63: 281-291
Tsou, P.L., Lee, S.Y., Allen, N.S., Winter-Sederoff, H. and Robertson, D. (2012) An ER-targeted calcium-binding peptide confers salt and drought tolerance mediated by CIPK6 in Arabidopsis. Planta, 235, (3), 539-552.
De Silva, K., Laska, B., Brown, C.S., Winter Sederoff, H., Khodakovskaya, M., (2011) Arabidopsis thaliana calcium-dependent lipid-binding protein (AtCLB): a novel repressor of abiotic stress response. J. Exp. Bot. Volume 62 (8): pp. 2679-2689.
Boss, W.F., Winter-Sederoff, H., Im, Y.J., Moran, N., Grunden, A., Perera, I.Y. (2010) Basal Signaling Regulates Plant Growth and Development. Plant Physiol. 154: 439-443.
Salinas-Mondragon, R., Kajla, J.D., Perera, I.Y., Brown, C.S., Winter Sederoff H. (2010) InsP3 turnover integrates the transcriptional response to gravity and light in Arabidopsis. Plant Cell and Environment, in press.
Novaes, E., Kirst, M., Chiang, V., Winter-Sederoff, H., Sederoff, R. (2010) Lignin, biomass and wood formation: a negative correlation for growth and lignin content. Plant Physiology, in press.
Khodakovskaya, M., Sword, C., Wu, Q., Perera, I.Y., Boss, W.F., Brown, C.S., Winter Sederoff, H. (2010) Increasing inositol (1,4,5)-trisphosphate metabolism affects drought tolerance, carbohydrate metabolism and phosphate-sensitive biomass increases in tomato. Plant Biotechnology Journal 8: 170-183.
Winter Sederoff, H., Perera, I.Y. (2010) Engineering Signal Transduction to Improve Abiotic Stress Response. pp. 8-10. In: Information Systems for Biotechnology (ISB) News Report, Virginia Polytechnic Institute and State University, Blacksburg, VA.
Howard, B.E., Sick, B. Perera, I., Im, Y.J., Winter Sederoff, H., Heber, S. (2007) Quality Assessment of Affymetrix GeneChip data using the EM algorithm and a naïve Bayes Classifier. Bioinformatics and Bioengineering (BIBE) 2007. Proceedings of the 7th IEEE International Conference, pp.145-150.
Brown, C.S., Winter Sederoff, H., Davies, E., Ferl, R.J., Stanković, B. (2007) Plant(s) for Space Exploration, pp. 183-196. In: Plant Tropisms, by P. Masson and S. Gilroy (eds.). Blackwell Publishing, Ames (IA).
Yester, J.W., Kimbrough, J.M., Salinas-Mondragon, R.E., Masson, P.H., Brown, C.S., Winter Sederoff, H. (2006) Regulation of transcription in roots of Arabidopsisgravity mutant. Gravitational and Space Biology 20: 159-160.
Salinas-Mondragon, R.E., Brogan, A., Ward, N., Perera, I.Y., Boss, W.F., Brown, C.S., Winter Sederoff, H. (2005) Gravity and Light: Integrating Transcriptional Regulation in Roots. Gravitational and Space Biology18: 121-123.
Kimbrough, J.M., Brown, C.S., Winter Sederoff, H. (2005) Co-expression and hormonal regulation of genes throughout gravity and mechanical stimulation in theArabidopsis root apex. Gravitational and Space Biology18: 117-119.
Kimbrough, J.M., Salinas-Mondragon, R., Boss, W.F., Brown, C.S., Winter Sederoff, H. (2004) The fast and transient transcriptional network of gravity and mechanical stimulation in the Arabidopsis root apex.Plant Physiology 136: 2790-2805.
Hardin, S. C., Winter, H., Huber, S.C. (2004). Phosphorylation of the amino terminus of maize sucrose synthase in relation to membrane association and enzyme activity. Plant Physiology 134: 1427-1438.
Hardin, S.C., Tang, G.-Q., Scholz, A., Holtgräwe, D., Winter, H., Huber, S.C. (2003) Serine-170 is a calcium-dependent protein kinase targeted phosphorylation site in sucrose synthase that is correlated with protein instability. Plant Journal 35: 588-603.
Smith, P.M.C., Winter, H., Storer, P.J., Bussell, J.D., Schuller, K.A., Atkins, C.A. (2002) Effect of short-term N2-deficiency on expression of the ureide pathway in cowpea root nodules. Plant Physiology 129: 1216-1221.
Winter, H., Huber, SC. (2000) Regulation of sucrose metabolism in higher plants. Critical Reviews in Biochemistry and Molecular Biology 35: 253-289.
Winter, H., Huber, SC. (2000) Regulation of sucrose metabolism in higher plants. Critical Reviews in Plant Science 19: 31-67. Reprinted from Critical Reviews in Biochemistry and Molecular Biology
Winter, H., Huber, S.C. (2000) Sucrose metabolism and the actin cytoskeleton, pp. 119-128. In: Actin: A Dynamic Framework for Multiple Plant Cell Functions, C.J. Staiger, F. Baluska, D. Volkmann, and P. Barlow (eds.). Kluwer Academic Publisher, Dordrecht, The Netherlands.
Huber, S.C., Kaiser, W.M., Toroser, D., Athwal, G.S., Winter, H., Huber, J.L. (1999) Regulation of sucrose metabolism by protein phosphorylation. Stimulation of sucrose synthesis by osmotic stress and 5- aminoimidazole-carboxamide riboside, pp. 61-67. In:Plant Carbohydrate Biochemistry, by J.A. Bryant, M.M. Burrel, and N.J. Kruger (eds.). BIOS-Publishers, Blackwood, UK.
Kuzma, M.M., Winter, H., Storer, P., Oresnik, I., Atkins, C.A., Layzell, D.B. (1999) The site of O2 limitation in soybean nodules. Plant Physiology 119: 399-408.
Collings, D.A., Winter, H., Wyatt, S.E., Allen, N.S. (1998) Growth dynamics and cytoskeleton organization during stem maturation and gravity-induced stem bending in Zea mays L. Planta 207: 246-258.
Winter, H., Huber, J.L., Huber, S.C. (1998) Identification of sucrose synthase as an actin-binding protein. FEBS Letters 430: 205-208.
Huber, S.C., McMicheal, R.W. Jr., Toroser, D., Bachmann, M., Athwal, G.S., Winter, H., Huber, J.L. (1998) Regulation of cytosolic metabolism by reversible seryl phosphorylation, pp. 101-107. In: Protein Phosphorylation in Plants, by P. Gadal, M. Kreis, M. Drom, J. Brulfert, C. Bergouniouy, and J. Vidal (eds.) University of Paris-Sud, Orsay, France.
Winter, H., Huber, J.L., Huber, S.C. (1997) Membrane association of sucrose synthase: Changes during the graviresponse and possible control by phosphorylation.FEBS Letters 420: 151-155.
Lohaus, G., Heineke D., Kruse, A., Leidreiter K., Riens, B., Robinson, D.G., Winter, H., Winzer, T., Heldt, H.-W. (1998) Compartmentation of metabolites between the subcellular compartments of leaves, the apoplast, the phloem and the storage tissue of different crop plants, pp. 159-172. In: Regulation of Primary Metabolic Pathways in Plants, by N. Krüber (ed.). Kluwer Academic Publisher, Dordrecht, The Netherlands.
Heineke, D., Lohaus, G., Winter, H. (1997) Compartmentation of C/N metabolism, pp. 205-218. In:A Molecular Approach to Primary Metabolism in Plants, by C.H. Foyer and P. Quick (eds.). Taylor and Francis, London, UK.
Wadham, C., Winter, H., Schuller, K.A. (1996) Regulation of soybean nodule phosphoenol-pyruvate carboxylase in vivo. Physiologia Plantarum 97: 531-535.
Lohaus, G., Winter, H., Riens, B., Heldt, H.W. (1995) Further studies of the phloem loading process in leaves of barley and spinach: The comparison of metabolite concentrations in the apoplastic compartment with those in the cytosolic compartment and in the sieve tubes.Botanica Acta 108: 270-275.
Leidreiter, K., Kruse, A., Riens, B., Winter, H., Lohaus, G., Robinson, D.G., Heineke, D., and Heldt, H.W. (1995) Subcellular compartmentation of metabolites in plant cells, pp. 483-486. In: Photosynthesis: From Light to Biosphere, by P. Mathis (ed.). Kluwer Academic Publisher, Dordrecht, The Netherlands.
Winter, H., Robinson, D., Heldt, H.W. (1994) Subcellular volumes and metabolite concentrations in spinach leaves. Planta 193: 530-535.
Hedrich, R., Marten, I., Lohse, G., Dietrich, P., Winter, H., Lohaus, G., Heldt, H.-W. (1994) -sensitive anion channels enable guard cells to sense changes in the ambient CO2 concentration. Plant Journal 6 (5): 741-748.
Riens, B., Lohaus, G., Winter, H., Heldt, H.W. (1994) Production and diurnal utilisation of assimilates in leaves of spinach (Spinacia oleracea) and barley (Hordeum vulgare). Planta 192: 479-501.
Winter, H., Robinson, D.G., Heldt, H.W. (1993) Subcellular volumes and metabolite concentrations in barley leaves. Planta 191: 180-190.
Winter, H., Lohaus, G., Heldt, H.W. (1992) Phloem transport of amino acids in relation to their cytosolic levels in barley leaves. Plant Physiology 99: 996-1004.