Diane Jofuku Okamuro
IOS Division of Integrative Organismal Systems
BIO Directorate for Biological Sciences
Start Date:
September 1, 2001
Expires:
August 31, 2007 (Estimated)
Awarded Amount to Date:
$3686432
Investigator(s):
Pedro Mendes mendes@vt.edu (Principal Investigator)
Richard Dixon (Co-Principal Investigator)
Sponsor:
Virginia Polytechnic Institute and State University
1880 Pratt Drive
BLACKSBURG, VA 24060 540/231-5281
NSF Program(s):
PLANT GENOME RESEARCH PROJECT
Field Application(s):
Program Reference Code(s):
BIOT, 9109, 7462
Program Element Code(s):
1329
ABSTRACT
Medicago truncatula is a close relative of the world's most important forage legume, alfalfa (Medicago sativa). It is a rich source of natural products, such as flavonoids, isoflavonoids and triterpenes, which impact its properties as a forage legume. The main experimental approach of this project is to perturb the expression of these natural products, and other areas of metabolism, by exposing cell cultures to biotic and abiotic elicitors. Use of cell suspension cultures will allow sufficient material to be collected and analyzed in parallel. Three experimental conditions have been chosen that mimic natural environmental challenges. The ultimate goal of this project is to generate a truly functional genomics data set for control and elicited cell cultures. Such data will encompass expressed sequence information and the associated mRNA, protein and metabolite identities and concentrations. This project will produce a variety of data so it becomes imperative to establish integrative models and software to facilitate relational analysis of the data to each other and to previous knowledge on sequences and pathways. Software is a facilitator of the discovery process when it enables the user to "navigate" the biological data in a dynamic and transparent way, requiring only the most basic computational skills. The bioinformatics component of this project will: i) construct a relational database to store all data; ii) construct an expandable analysis server that will facilitate processing the data with several statistical and numerical algorithms; and iii) integrate the above components through a web interface. The data as well as the software will be made available publicly.
The data generated by this project will be used to construct a quantitative predictive model of the time courses after elicitation, which is required to interpret the regulation of the underlying complex biological processes. The data will provide information about the extent and nature of gene expression reprogramming in response to biotic and abiotic signals at the transcription, translation and metabolic levels. There will also be practical applications in directed gene discovery for important agronomic traits involving plant natural products. Finally, this project will make available to the scientific community a bioinformatics system capable of supporting functional genomics ranging from the transcriptome to the metabolome.
PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH
Achnine, L; Huhman, DV; Farag, MA; Sumner, LW; Blount, JW; Dixon, RA. "Genomics-based selection and functional characterization of triterpene glycosyltransferases from the model legume Medicago truncatula," PLANT JOURNAL, v.41, 2005, p. 875-887.
Asirvatham, VS; Watson, BS; Sumner, LW. "Analytical and biological variances associated with proteomic studies of Medicago truncatula by two-dimensional polyacrylamide gel electrophoresis," PROTEOMICS, v.2, 2002, p. 960-968.
Bino, RJ; Hall, RD; Fiehn, O; Kopka, J; Saito, K; Draper, J; Nikolau, BJ; Mendes, P; Roessner-Tunali, U; Beale, MH; Trethewey, RN; Lange, BM; Wurtele, ES; Sumner, LW. "Potential of metabolomics as a functional genomics tool," TRENDS IN PLANT SCIENCE, v.9, 2004, p. 418-425.
Broeckling, CD; Huhman, DV; Farag, MA; Smith, JT; May, GD; Mendes, P; Dixon, RA; Sumner, LW. "Metabolic profiling of Medicago truncatula cell cultures reveals the effects of biotic and abiotic elicitors on metabolism," JOURNAL OF EXPERIMENTAL BOTANY, v.56, 2005, p. 323-336.
Broeckling, CD; Reddy, IR; Duran, AL; Zhao, XC; Sumner, LW. "MET-IDEA: Data extraction tool for mass spectrometry-based metabolomics," ANALYTICAL CHEMISTRY, v.78, 2006, p. 4334-4341.
Camacho, D., De La Fuente, A., Mendes P.. "The origin of correlations in metabolomics data," Metabolomics, v.1, 2005, p. 53.
de la Fuente, A.
Mendes, P.. "Integrative modeling of gene expression and cell metabolism.," Applied Bioinformatics, v.2, 2003, p. 79-90.
Deavours, BE; Liu, CJ; Naoumkina, MA; Tang, YH; Farag, MA; Sumner, LW; Noel, JP; Dixon, RA. "Functional analysis of members of the isoflavone and isoflavanone O-methyltransferase enzyme families from the model legume Medicago truncatula," PLANT MOLECULAR BIOLOGY, v.62, 2006, p. 715-733.
Dixon, R.A.
Sumner, L.W.. "Legume Natural Products: Understanding and manipulating complex pathways for human and animal health," Plant Physiology, v.131, 2003, p. 878.
Dixon, RA; Gang, DR; Charlton, AJ; Fiehn, O; Kuiper, HA; Reynolds, TL; Tjeerdema, RS; Jeffery, EH; German, JB; Ridley, WP; Seiber, JN. "Perspective - Applications of metabolomics in agriculture," JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY, v.54, 2006, p. 8984-8994.
Duran, A.L.
Yang, J.
Wang, L.
Sumner, L.W.. "Metabolomics Spectral Formatting, Alignment and Conversion Tools (MSFACTs)," Bioinformatics, v.19, 2003, p. 2283-2293.
Farag, MA; Huhman, DV; Lei, ZT; Sumner, LW. "Metabolic profiling and systematic identification of flavonoids and isoflavonoids in roots and cell suspension cultures of Medicago truncatula using HPLC-UV-ESI-MS and GC-MS," PHYTOCHEMISTRY, v.68, 2007, p. 342-354.
Fiehn, O; Kristal, B; Van Ommen, B; Sumner, LW; Sansone, SA; Taylor, C; Hardy, N; Kaddurah-Daouk, R. "Establishing reporting standards for metabolomic and metabonomic studies: A call for participation," OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY, v.10, 2006, p. 158-163.
Fiehn, O; Robertson, D; Griffin, J; van der Werf, M; Nikolau, B; Morrison, N; Sumner, LW; Goodacre, R; Hardy, NW; Taylor, C; Fostel, J; Kristal, B; Kaddurah-Daouk, R; Mendes, P; van Ommen, B; Lindon, JC; Sansone, SA. "The metabolomics standards initiative (MSI)," METABOLOMICS, v.3, 2007, p. 175-178.
Fiehn, O; Sumner, LW; Rhee, SY; Ward, J; Dickerson, J; Lange, BM; Lane, G; Roessner, U; Last, R; Nikolau, B. "Minimum reporting standards for plant biology context information in metabolomic studies," METABOLOMICS, v.3, 2007, p. 195-201.
Hucka, M; Finney, A; Sauro, HM; Bolouri, H; Doyle, JC; Kitano, H; Arkin, AP; Bornstein, BJ; Bray, D; Cornish-Bowden, A; Cuellar, AA; Dronov, S; Gilles, ED; Ginkel, M; Gor, V; Goryanin, II; Hedley, WJ; Hodgman, TC; Hofmeyr, JH; Hunter, PJ; Juty, NS; Kasber. "The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models," BIOINFORMATICS, v.19, 2003, p. 524-531.
Le Novere, N; Finney, A; Hucka, M; Bhalla, US; Campagne, F; Collado-Vides, J; Crampin, EJ; Halstead, M; Klipp, E; Mendes, P; Nielsen, P; Sauro, H; Shapiro, B; Snoep, JL; Spence, HD; Wanner, BL. "Minimum information requested in the annotation of biochemical models (MIRIAM)," NATURE BIOTECHNOLOGY, v.23, 2005, p. 1509-1515.
Lei, Z; Elmer, AM; Watson, BS; Dixon, RA; Mendes, PJ; Sumner, LW. "A two-dimensional electrophoresis proteomic reference map and systematic identification of 1367 proteins from a cell suspension culture of the model legume Medicago truncatula," MOLECULAR & CELLULAR PROTEOMICS, v.4, 2005, p. 1812-1825.
May, GD; Dixon, RA. "Medicago truncatula," CURRENT BIOLOGY, v.14, 2004, p. R180-R181.
Mendes, P.
Sha, W
Ye, K.. "Artificial gene networks for objective comparison of analysis algorithms," Bioinformatics, v.19, 2003, p. ii122.
Moles, CG; Mendes, P; Banga, JR. "Parameter estimation in biochemical pathways: A comparison of global optimization methods," GENOME RESEARCH, v.13, 2003, p. 2467-2474.
Naoumkina, M., Mohamed A. Farag, M.A., Sumner, L.W., Tang, Y., Liu, C.-J. and Dixon, R.A.. "Inaugural Article: Different mechanisms for phytoalexin induction by pathogen- and wound signals in Medicago truncatula," Proceedings of the National Academy of Sciences USA, v.104, 2007, p. 17909.
P. Mendes. "Emerging bioinformatics for the metabolome," Briefings in Bioinformatics, v.3, 2002, p. 134-145.
R. Hall
M. Beale
O. Fiehn
N. Hardy
L. Sumner
R. Bino. "Plant metabolomics as the missing link in functional genomics strategies," Plant Cell, v.14, 2002, p. 1437-1440.
Sansone, SA; Fan, T; Goodacre, R; Griffin, JL; Hardy, NW; Kaddurah-Daouk, R; Kristal, BS; Lindon, J; Mendes, P; Morrison, N; Nikolau, B; Robertson, D; Sumner, LW; Taylor, C; van der Werf, M; van Ommen, B; Fiehn, O. "The metabolomics standards initiative," NATURE BIOTECHNOLOGY, v.25, 2007, p. 844-848.
Sumner, LW; Mendes, P; Dixon, RA. "Plant metabolomics: large-scale phytochemistry in the functional genomics era," PHYTOCHEMISTRY, v.62, 2003, p. 817-836.
Suzuki, H; Achnine, L; Xu, R; Matsuda, SPT; Dixon, RA. "A genomics approach to the early stages of triterpene saponin biosynthesis in Medicago truncatula," PLANT JOURNAL, v.32, 2002, p. 1033-1048.
Suzuki, H; Reddy, MSS; Naoumkina, M; Aziz, N; May, GD; Huhman, DV; Sumner, LW; Blount, JW; Mendes, P; Dixon, RA. "Methyl jasmonate and yeast elicitor induce differential transcriptional and metabolic re-programming in cell suspension cultures of the model legume Medicago truncatula," PLANTA, v.220, 2005, p. 696-707.
Watson, BS; Asirvatham, VS; Wang, LJ; Sumner, LW. "Mapping the proteome of barrel medic (Medicago truncatula)," PLANT PHYSIOLOGY, v.131, 2003, p. 1104-1123.
Williams, BJ; Cameron, CJ; Workman, R; Broeckling, CD; Sumner, LW; Smith, JT. "Amino acid profiling in plant cell cultures: An inter-laboratory comparison of CE-MS and GC-MS," ELECTROPHORESIS, v.28, 2007, p. 1371-1379.
