Granger causality in integrated GC-MS and LC-MS metabolomics data reveals the interface of primary and secondary metabolism

Metabolomics

Volumn 9, Issue 3, 2013, Pages 564-574

  Doerfler, Hannes ^a   Lyon, David ^a   Nägele, Thomas ^a   Sun, Xiaoliang ^a   Fragner, Lena ^a   Hadacek, Franz ^a   Egelhofer, Volker ^a   Weckwerth, Wolfram ^a  

^a UNIVERSITY OF VIENNA   (Austria)

Author keywords

Cold acclimation; Differential Jacobian; Granger causality; Mass spectrometry; Metabolomics; Plant systems biology

Indexed keywords

PHENYLALANINE; TRYPTOPHAN;

ARABIDOPSIS THALIANA; ARTICLE; CARBOHYDRATE METABOLISM; COLD EXPOSURE; CONTROLLED STUDY; CORRELATION ANALYSIS; DIFFERENTIAL JACOBIAN MATRIX; GRANGER CAUSALITY; LIQUID CHROMATOGRAPHY; LOW TEMPERATURE; MASS FRAGMENTOGRAPHY; MASS SPECTROMETRY; MASS TO CHARGE RATIO; MATHEMATICAL ANALYSIS; MATHEMATICAL MODEL; METABOLITE; METABOLOMICS; NONHUMAN; PHYSICAL PARAMETERS; STATISTICAL ANALYSIS;

EID: 84877605157     PISSN: 15733882     EISSN: 15733890     Source Type: Journal    
DOI: 10.1007/s11306-012-0470-0     Document Type: Article

References (32)

1. Bloor, S. J., & Abrahams, S. (2002). The structure of the major anthocyanin in Arabidopsis thaliana. Phytochemistry, 59, 343-346.
2. Giersch, C. (2000). Mathematical modelling of metabolism. Current Opinion in Plant Biology, 3, 249-253.
3. Granger, C. (1969). Investigating causal relations by econometric models and cross-spectral methods. Econometrica, 37, 414-426.
4. Havaux, M., & Kloppstech, K. (2001). The protective functions of carotenoid and flavonoid pigments against excess visible radiation at chilling temperature investigated in Arabidopsis npq and tt mutants. Planta, 213, 953-966.
5. Hoehenwarter, W., van Dongen, J. T., Wienkoop, S., Steinfath, M., Hummel, J., Erban, A., et al. (2008). A rapid approach for phenotype-screening and database independent detection of cSNP/protein polymorphism using mass accuracy precursor alignment. Proteomics, 8, 4214-4225.
6. Klotke, J., Kopka, J., Gatzke, N., & Heyer, A. G. (2004). Impact of soluble sugar concentrations on the acquisition of freezing tolerance in accessions of Arabidopsis thaliana with contrasting cold adaptation-evidence for a role of raffinose in cold acclimation. Plant, Cell and Environment, 27, 1395-1404.
7. Kopka, J., Schauer, N., Krueger, S., Birkemeyer, C., Usadel, B., Bergmuller, E., et al. (2005). GMD@CSB. DB: the Golm Metabolome database. Bioinformatics, 21(8), 1635-1638.
8. Matsuda, F., Yonekura-Sakakibara, K., Niida, R., Kuromori, T., Shinozaki, K., & Saito, K. (2009). MS/MS spectral tag-based annotation of non-targeted profile of plant secondary metabolites. The Plant Journal, 57, 555-577.
9. Moing, A., Aharoni, A., Biais, B., Rogachev, I., Meir, S., Brodsky, L., et al. (2011). Extensive metabolic cross-talk in melon fruit revealed by spatial and developmental combinatorial metabolomics. New Phytologist, 190, 683-696.
10. Morgan, J. A., & Rhodes, D. (2002). Mathematical modeling of plant metabolic pathways. Metabolic Engineering, 4, 80-89.
11. Nägele, T., Henkel, S., Hörmiller, I., Sauter, T., Sawodny, O., Ederer, M., et al. (2010). Mathematical modelling of the central carbohydrate metabolism in Arabidopsis thaliana reveals a substantial regulatory influence of vacuolar invertase on whole plant carbon metabolism. Plant Physiology, 153, 260-272.
12. Nägele, T., Stutz, S., Hörmiller, I. I., & Heyer, A. G. (2012). Identification of a metabolic bottleneck for cold acclimation in Arabidopsis thaliana. The Plant Journal,. doi: 10. 1111/j. 1365-313X. 2012. 05064. x.
13. Nägele, T., & Weckwerth, W. (2012). Mathematical modeling of plant metabolism-from reconstruction to prediction. Metabolites, 2(3), 553-566.
14. Page, M., Sultana, N., Paszkiewicz, K., Florance, H., & Smirnoff, N. (2012). The influence of ascorbate on anthocyanin accumulation during high light acclimation in Arabidopsis thaliana: further evidence for redox control of anthocyanin synthesis. Plant, Cell and Environment, 35, 388-404.
15. Rios-Estepa, R., & Lange, B. M. (2007). Experimental and mathematical approaches to modeling plant metabolic networks. Phytochemistry, 68, 2351-2374.
16. Scherling, C., Roscher, C., Giavalisco, P., et al. (2010). Metabolomics unravel contrasting effects of biodiversity on the performance of individual plant species. PLoS ONE, 5, e12569.
17. Shi, M.-Z., & Xie, D.-Y. (2010). Features of anthocyanin biosynthesis in pap1-D and wild-type Arabidopsis thaliana plants grown in different light intensity and culture media conditions. Planta, 231(6), 1385-1400.
18. Steuer, R., Kurths, J., Fiehn, O., & Weckwerth, W. (2003). Observing and interpreting correlations in metabolomic networks. Bioinformatics, 19, 1019-1026.
19. Sun, X., & Weckwerth, W. (2012). COVAIN: a toolbox for uni- and multivariate statistics, time-series and correlation network analysis and inverse estimation of the differential Jacobian from metabolomics covariance data. Metabolomics, 8, 81-93. doi: 10. 1007/s11306-012-0399-3.
20. Tohge, T., Nishiyama, Y., Hirai, M. Y., Yano, M., Nakajima, J., Awazuhara, M., et al. (2005). Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over-expressing an MYB transcription factor. The Plant Journal, 42, 218-235.
21. Tsai, F., & Coruzzi, G. (1991). Light represses transcription of asparagine synthetase genes in photosynthetic and nonphotosynthetic organs of plants. Molecular and Cellular Biology, 11, 4966-4972.
22. Tzin, V., & Galili, G. (2010). New insights into the shikimate and aromatic amino acids biosynthesis pathways in plants. Molecular Plant, 3, 956-972.
23. Tzin, V., Malitsky, S., Aharoni, A., & Galili, G. (2009). Expression of a bacterial bi-functional chorismate mutase/prephenate dehydratase modulates primary and secondary metabolism associated with aromatic amino acids in Arabidopsis. The Plant Journal, 60, 156-167.
24. Tzin, V., Malitsky, S., Ben Zvi, M. M., Bedair, M., Sumner, L., Aharoni, A., et al. (2012). Expression of a bacterial feedback-insensitive 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase of the shikimate pathway in Arabidopsis elucidates potential metabolic bottlenecks between primary and secondary metabolism. New Phytologist, 194(2), 430-439.
25. Usadel, B., Bläsing, O. E., Gibon, Y., Poree, F., Höhne, M., Günter, M., et al. (2008). Multilevel genomic analysis of the response of transcripts, enzyme activities and metabolites in Arabidopsis rosettes to a progressive decrease of temperature in the non-freezing range. Plant, Cell and Environment, 31, 518-547.
26. Walther, D., Strassburg, K., Durek, P., & Kopka, J. (2010). Metabolic pathway relationships revealed by an integrative analysis of the transcriptional and metabolic temperature stress-response dynamics in yeast. OMICS, 14, 261-274.
27. Waridel, P., Wolfender, J.-L., Ndjoko, K., Hobby, K. R., Major, H. J., & Hostettmann, K. (2001). Evaluation of quadrupole time-of-flight tandem mass spectrometry and ion-trap multiple-stage mass spectrometry for the differentiation of C-glycosidic flavonoid isomers. Journal of Chromatography A, 926, 29-41.
28. Weckwerth, W. (2003). Metabolomics in systems biology. Annual Review of Plant Biology, 54, 669-689.
29. Weckwerth, W. (2011a). Green systems biology-from single genomes, proteomes and metabolomes to ecosystems research and biotechnology. Journal of Proteomics, 75, 284-305.
30. Weckwerth, W. (2011b). Unpredictability of metabolism-the key role of metabolomics science in combination with next-generation genome sequencing. Analytical and Bioanalytical Chemistry, 400, 1967-1978.
31. Weckwerth, W., Wenzel, K., & Fiehn, O. (2004). Process for the integrated extraction identification, and quantification of metabolites, proteins and RNA to reveal their co-regulation in biochemical networks. Proteomics, 4, 78-83.
32. Winkel-Shirley, B. (2002). Biosynthesis of flavonoids and effects of stress. Current Opinion in Plant Biology, 5, 218-223.