Novel quantitative metabolomic approach for the study of stress responses of plant root metabolism

Journal of Proteome Research

Volumn 13, Issue 12, 2014, Pages 5879-5887

  Li, Kefeng ^a,b   Wang, Xu ^c,d   Pidatala, Venkataramana R ^b   Chang, Chi Peng ^d   Cao, Xiaohong ^c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b MICHIGAN TECHNOLOGICAL UNIVERSITY   (United States)

^c TIANJIN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^d AmCellGene Co   (China)

Author keywords

Escherichia coli; maize; Pb stress; quantitative metabolomics; Saccharomyces cerevisiae; uniformly 13C labeled metabolites

Indexed keywords

CARBON 13; LEAD; PHOSPHOLIPID; PURINE; PYRIMIDINE;

ABIOTIC STRESS; ARTICLE; CHEMICAL LABELING; CONTROLLED STUDY; ESCHERICHIA COLI; GLYCOLYSIS; LIQUID CHROMATOGRAPHY; MAIZE; METABOLOMICS; NONHUMAN; PLANT METABOLISM; PLANT ROOT; SACCHAROMYCES CEREVISIAE; TANDEM MASS SPECTROMETRY; DRUG EFFECTS; METABOLISM; METABOLOME; PHYSIOLOGICAL STRESS;

ESCHERICHIA COLI; SACCHAROMYCES CEREVISIAE; ZEA MAYS;

LEAD; METABOLOME; METABOLOMICS; PLANT ROOTS; STRESS, PHYSIOLOGICAL; TANDEM MASS SPECTROMETRY; ZEA MAYS;

EID: 84915751034     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr5007813     Document Type: Article

References (32)

1. Patti, G. J.; Yanes, O.; Siuzdak, G. Innovation: Metabolomics: The apogee of the omics trilogy Nat. Rev. Mol. Cell Biol. 2012, 13, 263-269
2. Roberts, L. D.; Souza, A. L.; Gerszten, R. E.; Clish, C. B. Targeted Metabolomics Curr. Protoc. Mol. Biol. 2012, 10.1002/0471142727.mb3002s98
3. Segarra, G.; Jáuregui, O.; Casanova, E.; Trillas, I. Simultaneous quantitative LC-ESI-MS/MS analyses of salicylic acid and jasmonic acid in crude extracts of Cucumis sativus under biotic stress Phytochemistry 2006, 67, 395-401
4. Jin, X.; Wang, R. S.; Zhu, M.; Jeon, B. W.; Albert, R.; Chen, S.; Assmann, S. M. Abscisic acid-responsive guard cell metabolomes of Arabidopsis wild-type and gpa1 G-protein mutants Plant Cell 2013, 25, 4789-4811
5. Ciccimaro, E.; Blair, I. A. Stable-isotope dilution LC-MS for quantitative biomarker analysis Bioanalysis 2010, 2, 311-341
6. Birkemeyer, C.; Luedemann, A.; Wagner, C.; Erban, A.; Kopka, J. Metabolome analysis: The potential of in vivo labeling with stable isotopes for metabolite profiling Trends Biotechnol. 2005, 23, 28-33
7. Krijgsveld, J.; Ketting, R. F.; Mahmoudi, T.; Johansen, J.; Artal-Sanz, M.; Verrijzer, C. P.; Plasterk, R. H.; Heck, A. J. Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics Nat. Biotechnol. 2003, 21, 927-931
8. Gouw, J. W.; Krijgsveld, J.; Heck, A. J. Quantitative proteomics by metabolic labeling of model organisms Mol. Cell Proteomics 2010, 9, 11-24
9. Bennett, B. D.; Kimball, E. H.; Gao, M.; Osterhout, R.; Van Dien, S. J.; Rabinowitz, J. D. Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli Nat. Chem. Biol. 2009, 5, 593-599
10. 13C labeled internal standard Anal. Bioanal. Chem. 2014, 406, 915-922
11. Yanes, O.; Tautenhahn, R.; Patti, G. J.; Siuzdak, G. Expanding coverage of the metabolome for global metabolite profiling Anal. Chem. 2011, 83, 2152-2161
12. Li, K.; Pidatala, V. R.; Shaik, R.; Datta, R.; Ramakrishna, W. Integrated metabolomic and proteomic approaches dissect the effect of metal-resistant bacteria on maize biomass and copper uptake Environ. Sci. Technol. 2014, 48, 1184-1193
13. Bergman, L. W. Growth and maintenance of yeast Methods Mol. Biol. 2001, 177, 9-14
14. Lakshmanan, M.; Zhang, Z.; Mohanty, B.; Kwon, J. Y.; Choi, H. Y.; Nam, H. J.; Kim, D. I.; Lee, D. Y. Elucidating rice cell metabolism under flooding and drought stresses using flux-based modeling and analysis Plant Physiol. 2013, 162, 2140-2150
15. Windram, O.; Penfold, C. A.; Denby, K. J. Network Modeling to Understand Plant Immunity. Annu. Rev. Phytopathol. 2014, 52, 10.1146/annurev-phyto-102313-050103.
16. Shaik, R.; Ramakrishna, W. Machine learning approaches distinguish multiple stress conditions using stress-responsive genes and identify candidate genes for broad resistance in rice Plant Physiol. 2014, 164, 481-495
17. Alcazar, R.; Altabella, T.; Marco, F.; Bortolotti, C.; Reymond, M.; Koncz, C.; Carrasco, P.; Tiburcio, A. F. Polyamines: Molecules with regulatory functions in plant abiotic stress tolerance Planta 2010, 231, 1237-1249
18. Arbona, V.; Manzi, M.; Ollas, Cd; Gómez-Cadenas, A. Metabolomics as a tool to investigate abiotic stress tolerance in plants Int. J. Mol. Sci. 2013, 14, 4885-4911
19. Schwalbe-Herrmann, M.; Willmann, J.; Leibfritz, D. Separation of phospholipid classes by hydrophilic interaction chromatography detected by electrospray ionization mass spectrometry J. Chromatogr. A 2010, 1217, 5179-5183
20. Brouwers, J. F. Liquid chromatographic-mass spectrometric analysis of phospholipids. Chromatography, ionization and quantification Biochim. Biophys. Acta 2011, 1811, 763-775
21. Zhu, C.; Dane, A.; Spijksma, G.; Wang, M.; van der Greef, J.; Luo, G.; Hankemeier, T.; Vreeken, R. J. An efficient hydrophilic interaction liquid chromatography separation of 7 phospholipid classes based on a diol column J. Chromatogr. A 2012, 1220, 26-34
22. Bajad, S. U.; Lu, W.; Kimball, E. H.; Yuan, J.; Peterson, C.; Rabinowitz, J. D. Separation and quantitation of water soluble cellular metabolites by hydrophilic interaction chromatography-tandem mass spectrometry J. Chromatogr. A 2006, 1220, 76-88
23. Bennett, B. D.; Yuan, J.; Kimball, E. H.; Rabinowitz, J. D. Absolute quantitation of intracellular metabolite concentrations by an isotope ratio-based approach Nat. Protoc. 2008, 3, 1299-1311
24. 13C cell extract of Pichia pastoris -A powerful tool for evaluation of sample preparation in metabolomics J. Sep. Sci. 2012, 35, 3091-3105
25. 13C-labeled extracts. A new method for accurate quantification of changes in concentrations of intracellular metabolites Biotechnol. Bioeng. 2004, 85, 620-628
26. Li, K.; Pidatala, R. R.; Ramakrishna, W. Mutational, proteomic and metabolomic analysis of a plant growth promoting copper-resistant Pseudomonas spp FEMS Microbiol. Lett. 2012, 335, 140-148
27. Dresler, S.; Hanaka, A.; Bednarek, W.; Maksymiec, W. Accumulation of low-molecular-weight organic acids in roots and leaf segments of Zea mays plants treated with cadmium and copper Acta Physiol. Plant 2014, 36, 1565-1575
28. Gill, S. S.; Tuteja, N. Reactive oxygen species and antioxidant machinery in abiotic stress tolerance in crop plants Plant Physiol. Biochem. 2010, 48, 909-930
29. Testerink, C.; Munnik, T. Molecular, cellular, and physiological responses to phosphatidic acid formation in plants J. Exp. Bot. 2011, 62, 2349-2361
30. McLoughlin, F.; Testerink, C. Phosphatidic acid, a versatile water-stress signal in roots Front Plant Sci. 2013, 4, 525
31. Gasulla, F.; Vom Dorp, K.; Dombrink, I.; Zahringer, U.; Gisch, N.; Dormann, P.; Bartels, D. The role of lipid metabolism in the acquisition of desiccation tolerance in Craterostigma plantagineum: A comparative approach Plant J. 2013, 75, 726-741
32. Wang, X. The role of phospholipase D in signaling cascades Plant Physiol. 1999, 120, 645-652