Absolute quantification of metabolites in tomato fruit extracts by fast 2D NMR

Metabolomics

Volumn 11, Issue 5, 2015, Pages 1231-1242

  Jézéquel, Tangi ^a,b   Deborde, Catherine ^b,c   Maucourt, Mickaël ^b,c   Zhendre, Vanessa ^b   Moing, Annick ^b,c   Giraudeau, Patrick ^a,d  

^a UNIVERSITÉ DE NANTES   (France)

^b Bordeaux Functional Genomic Center   (France)

^c Univ Bordeaux   (France)

^d INSTITUT UNIVERSITAIRE DE FRANCE   (France)

Author keywords

COSY; Extracts; NMR; Quantitative analysis; Tomato; Ultrafast 2D NMR

Indexed keywords

PLANT EXTRACT; TOMATO FRUIT EXTRACT; UNCLASSIFIED DRUG;

ARTICLE; FOURIER TRANSFORMATION; INFORMATION PROCESSING; MEASUREMENT REPEATABILITY; METABOLITE; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; QUANTITATIVE ANALYSIS; RELAXATION TIME; SENSITIVITY ANALYSIS; SIGNAL NOISE RATIO; TOMATO;

EID: 84941023055     PISSN: 15733882     EISSN: 15733890     Source Type: Journal    
DOI: 10.1007/s11306-015-0780-0     Document Type: Article

References (60)

1. Allwood, J. W., de Vos, C. H. R., Moing, A., Deborde, C., Erban, A., Kopka, J., et al. (2011). Plant metabolomics and its potential for systems biology research: Background concepts, technology and methodology. Methods in Enzymology,500, 299–336.
2. Aue, W. P., Bartholdi, E., & Ernst, R. R. (1976). Two-dimensional spectroscopy. Application to nuclear magnetic resonance. Journal of Chemical Physics,64, 2229–2246.
3. Beauvoit, B. P., Colombié, S., Monier, A., Andrieu, M., Biais, B., Bénard, C., et al. (2014). Model-assisted analysis of sugar metabolism throughout tomato fruit development reveals enzyme and carrier properties in relation to vacuole expansion. Plant Cell,26, 3224–3242.
4. Beckonert, O., Keun, H. C., Ebbels, T. M. D., Bundy, J., Holmes, E., Lindon, J. C., & Nicholson, J. K. (2007). Metabolic profiling, metabolomic and metabonomic procedures for NMR spectroscopy of urine, plasma, serum and tissue extracts. Nature Protocols,2, 2692–2703.
5. Biais, B., Bénard, C., Beauvoit, B., Colombié, S., Prodhomme, D., Ménard, G., et al. (2014). Remarkable reproducibility of enzyme activity profiles in tomato fruits grown under contrasting environments provides a roadmap for studies of fruit metabolism. Plant Physiology,164, 1204–1221.
6. Bingol, K., Zhang, F., Brüschweiler-Li, L., & Brüschweiler, R. (2013). Quantitative analysis of metabolic mixtures by two-dimensional 13C constant-time TOCSY NMR spectroscopy. Analytical Chemistry,85, 6414–6420.
7. Boggio, S. B., Palatnik, J. F., Heldt, H. W., & Valle, E. M. (2000). Changes in amino acid composition and nitrogen metabolizing enzymes in ripening fruits of Lycopersicon esculentum Mill. Plant Science,159, 125–133.
8. Carrari, F., Baxter, C., Usadel, B., Urbanczyk-Wochniak, E., Zanor, M.-I., Nunes-Nesi, A., et al. (2006). Integrated analysis of metabolite and transcript levels reveals the metabolic shifts that underlie tomato fruit development and highlight regulatory aspects of metabolic network behavior. Plant Physiology,142, 1380–1396.
9. Carrari, F., & Fernie, A. R. (2006). Metabolic regulation underlying tomato fruit developement. Journal of Experimental Botany,57, 1883–1897.
10. Colombié, S., Nazaret, C., Bénard, C., Biais, B., Mengin, V., Solé, M., et al. (2015). Modelling central metabolic fluxes by constraint-based optimization reveals metabolic reprogramming of developing tomato fruit. Plant Journal,81, 24–39.
11. de Vos, R. C. H., Hall, R., Moing, A. (2011). Metabolomics of a model fruit: tomato. In: Hall, R. (ed) Biology of plant metabolomics. Annual plant reviews, vol 43. (pp. 109–115). Oxford: Wiley-Blackwell Ltd.
12. Deborde, C., Maucourt, M., Baldet, P., Bernillon, S., Biais, B., Talon, G., et al. (2009). Proton NMR quantitative profiling for quality assessment of greenhouse-grown tomato fruit. Metabolomics,5, 183–198.
13. Frydman, L., Lupulescu, A., & Scherf, T. (2003). Principles and features of single-scan two-dimensional NMR spectroscopy. Journal of the American Chemical Society,125, 9204–9217.
14. Frydman, L., Scherf, T., & Lupulescu, A. (2002). The acquisition of multidimensional NMR spectra within a single scan. Proceedings of the National Academy of Sciences United States of America,99, 15858–15862.
15. Gal, M., Frydman, L. (2010). Ultrafast multidimensional NMR: principles and practice of single-scan methods. In: Morris, G. A., J. W. Emsley (eds) Encyclopedia of magnetic resonance. (pp. 43–60). Chichester: Wiley.
16. Giovannoni, J. (2001). Molecular biology of fruit maturation and ripening. Annual Review of Plant Physiology and Plant Molecular Biology,52, 725–749.
17. Giraudeau, P. (2014). Quantitative 2D liquid-state NMR. Magnetic Resonance in Chemistry,52, 259–272.
18. Giraudeau, P., & Akoka, S. (2011). Sensitivity and lineshape improvement in ultrafast 2D NMR by optimized apodization in the spatially encoded dimension. Magnetic Resonance in Chemistry,49, 307–313.
19. Giraudeau, P., & Akoka, S. (2013). Fast and ultrafast quantitative 2D NMR: Vital tools for efficient metabolomic approaches. Advances in Botanical Research,67, 99–158.
20. Giraudeau, P., & Frydman, L. (2014). Ultrafast 2D NMR: An emerging tool in analytical spectroscopy. Annual Review of Analytical Chemistry,7, 129–161.
21. Giraudeau, P., Massou, S., Robin, Y., Cahoreau, E., Portais, J.-C., & Akoka, S. (2011). Ultrafast quantitative 2D NMR: An efficient tool for the measurement of specific isotopic enrichments in complex biological mixtures. Analytical Chemistry,83, 3112–3119.
22. Giraudeau, P., Remaud, G. S., & Akoka, S. (2009). Evaluation of ultrafast 2D NMR for quantitative analysis. Analytical Chemistry,81, 479–484.
23. Gronwald, W., Klein, M. S., Kaspar, H., Fagerer, S. R., Nurnberger, N., Dettmer, K., et al. (2008). Urinary metabolite quantification employing 2D NMR spectroscopy. Analytical Chemistry,80, 9288–9297.
24. Holzgrabe, U. (2010). Quantitative NMR spectroscopy in pharmaceutical applications. Progress in Nuclear Magnetic Resonance Spectroscopy,57, 229–240.
25. Hu, F., Furihata, K., Kato, Y., & Tanokura, M. (2007). Nondestructive quantification of organic compounds in whole milk without pretreatment by two-dimensional NMR spectroscopy. Journal of Agriculture and Food Chemistry,55, 4307–4311.
26. ICH-Q2(R1) (1995). Validation of analytical procedures: text and methodology. http://www.ich.org/products/guidelines/quality/article/quality-guidelines.html.
27. Jeener, J. (1971). Lecture presented at Ampere International Summer School II. Yugoslavia: Basko Polje.
28. Kazimierczuk, K., Stanek, J., Zawadzka-Kazimierczuk, A., & Koźmiński, W. (2010). Random sampling in multidimensional NMR spectroscopy. Progress in Nuclear Magnetic Resonance Spectroscopy,57, 420–434.
29. Koskela, H. (2009). Quantitative 2D NMR studies. Annual Reports on NMR Spectroscopy,66, 1–31.
30. Krishnan, P., Kruger, N. J., & Ratcliffe, R. G. (2005). Metabolite fingerprinting and profiling in plants using NMR. Journal of Experimental Botany,56, 255–265.
31. Kruger, N. J., Troncoso-Ponce, M. A., & Ratcliffe, R. G. (2008). 1H NMR metabolite fingerprinting and metabolomic analysis of perchloric acid extracts from plant tissues. Nature Protocols,3, 1001–1012.
32. Kupce, E., & Freeman, R. (2003). Two-dimensional Hadamard spectroscopy. Journal of Magnetic Resonance,162, 300–310.
33. Kupce, E., & Freeman, R. (2007). Fast multidimensional NMR by polarization sharing. Magnetic Resonance in Chemistry,45, 2–4.
34. Le Gall, G., Colquhoun, I. J., Davis, A. L., Collins, G. J., & Verhoeyen, M. E. (2003). Metabolite profiling of tomato (Lycopersicon esculentum) Using 1H NMR spectroscopy as a tool to detect potential unintended effects following a genetic modification. Journal of Agriculture and Food Chemistry,51, 2447–2456.
35. Le Guennec, A., Giraudeau, P., & Caldarelli, S. (2014). Evaluation of fast 2D NMR for metabolomics. Analytical Chemistry,86, 5946–5954.
36. Le Guennec, A., Tea, I., Antheaume, I., Martineau, E., Charrier, B., Pathan, M., et al. (2012). Fast determination of absolute metabolite concentrations by spatially-encoded 2D NMR: Application to breast cancer cell extracts. Analytical Chemistry,84, 10831–10837.
37. Lewis, I. A., Schommer, S. C., Hodis, B., Robb, K. A., Tonelli, M., Westler, W., et al. (2007). Method for determining molar concentrations of metabolites in complex solutions from two-dimensional 1H-13C NMR spectra. Analytical Chemistry,79, 9385–9390.
38. Ludwig, C., & Viant, M. R. (2010). Two-dimensional J-resolved NMR spectroscopy: Review of a key methodology in the metabolomics toolbox. Phytochemical Analysis,21, 22–32.
39. Malz, F., & Jancke, H. (2005). Validation of quantitative NMR. Journal of Pharmaceutical and Biomedical Analysis,38, 813–823.
40. Martineau, E., Tea, I., Akoka, S., & Giraudeau, P. (2012). Absolute quantification of metabolites in breast cancer cell extracts by quantitative 2D 1H INADEQUATE NMR. NMR in Biomedicine,25, 985–992.
41. Moing, A., Maucourt, M., Renaud, C., Gaudillere, M., Brouquisse, R., Lebouteiller, B., et al. (2004). Quantitative metabolic profiling by one-dimensional H-1-NMR analyses: Application to plant genetics and functional genomics. Functional Plant Biology,31, 889–902.
42. Morris, G. A. (1992). Systematic sources of signal irreproducibility and t1 noise in high field NMR spectrometers. Journal of Magnetic Resonance,100, 316–328.
43. Mounet, F., Lemaire-Chamley, M., Maucourt, M., Cabasson, C., Giraudel, J., Deborde, C., et al. (2007). Quantitative metabolic profiles of tomato flesh and seeds during fruit development: Complementary analysis with ANN and PCA. Metabolomics,3, 273–288.
44. Nielsen, J., & Oliver, S. (2005). The next wave in metabolome analysis. Trends in Biotechnology,23, 544–546.
45. Pathan, M., Akoka, S., Tea, I., Charrier, B., & Giraudeau, P. (2011). Multi-scan single shot” quantitative 2D NMR: A valuable alternative to fast conventional quantitative 2D NMR. Analyst,136, 3157–3163.
46. Pathan, M., Charrier, B., Tea, I., Akoka, S., & Giraudeau, P. (2013). New practical tools for the implementation and use of ultrafast 2D NMR experiments. Magnetic Resonance in Chemistry,51, 168–175.
47. Queiroz Junior, L. H. K., Ferreira, A. G., & Giraudeau, P. (2013). Optimization and practical implementation of ultrafast 2D NMR experiments. Quimica Nova,26, 577–581.
48. Ravanbakhsh, S., Liu, P., Bjorndahl, T., Mandal, R., Grant, J. R., Wilson, M., Eisner, R., Sinelnikov, I., Hu, X., Luchinat, C., Greiner, R., Wishart, D. S. (2014). Accurate, fully-automated NMR spectral profiling for metabolomics. arXiv:14091456v3 http://arxiv.org/abs/14091456v3.
49. Rouger, L., Charrier, B., Pathan, M., Akoka, S., & Giraudeau, P. (2014). Processing strategies to obtain clean interleaved ultrafast 2D NMR spectra. Journal of Magnetic Resonance,238, 87–93.
50. Schanda, P. (2009). Fast-pulsing longitudinal relaxation optimized techniques: Enriching the toolbox of fast biomolecular NMR spectroscopy. Progress in Nuclear Magnetic Resonance Spectroscopy,55, 238–265.
51. Schanda, P., Van Melckebeke, H., & Brutscher, B. (2006). Speeding up three-dimensional protein NMR experiments to a few minutes. Journal of the American Chemical Society,128, 9042–9043.
52. Schulze-Sünninghausen, D., Becker, J., & Luy, B. (2014). Rapid heteronuclear single quantum correlation NMR spectra at natural abundance. Journal of the American Chemical Society,136, 1242–1245.
53. Shrot, Y., & Frydman, L. (2009). Spatial/spectral encoding of the spin interactions in ultrafast multidimensional NMR. Journal of Chemical Physics,131, 224516.
54. Slupsky, C. M., Rankin, K. N., Wagner, J., Fu, H., Chang, D., Weljie, A. M., et al. (2007). Investigations of the effects of gender, diurnal variation and age in human urinary metabolomic profiles. Analytical Chemistry,79, 6995–7004.
55. Tal, A., & Frydman, L. (2010). Single-scan multidimensional magnetic resonance. Progress in Nuclear Magnetic Resonance Spectroscopy,57, 241–292.
56. Tredwell, G. D., Behrends, V., Geier, F. M., Liebeke, M., & Bundy, J. G. (2011). Between-person comparison of metabolite fitting for NMR-based quantitative metabolomics. Analytical Chemistry,83, 8683–8687.
57. Vitorge, B., Bieri, S., Humam, M., Christen, P., Hostettmann, K., Munoz, O., et al. (2009). High-precision heteronuclear 2D NMR experiments using 10-ppm spectral window to resolve carbon overlap. Chemical Communications, (8), 950–952.
58. Weljie, A. M., Newton, J., Mercier, P., Carlson, E., & Slupsky, C. M. (2006). Targeted profiling: Quantitative analysis of 1H NMR metabolomics data. Analytical Chemistry,78, 4430–4442.
59. Wishart, D. S. (2008). Quantitative metabolomics using NMR. Trac-Trends in Analytical Chemistry,27, 228–237.
60. Zulak, K. G., Weljie, A. M., Vogel, H. J., & Facchini, P. J. (2008). Quantitative 1H NMR metabolomics reveals extensive metabolic reprogramming of primary and secondary metabolism in elicitor-treated opium poppy cell cultures. BMC Plant Biology,8, 5.