Metabolome, yeast

Castrillo, J. L. Hayes, A. Mohammed, S. Gaskell, S. J. Oliver, S. G. An optimized protocol for metabolome analysis in yeast using direct infusion electrospray mass spectrometry. Phytochemistry 2003, 62, 929-937. 

Son, H. S., Hwang, G. S., Park, W. M., Hong, Y. S., and Lee, C. H. (2009c). Metabolomic characterization of malolactic fermentation and fermentative behaviors of wine yeast in grape wine.. Agric. Food Chem. 57, 4801-4809. 

Raamsdonk and colleagues set out to develop a metabolomics method that could be used to characterize proteins of unknown function in yeast [14]. Using an NMR approach they analyzed intracellular metabolites in mutants of Saccharomyces cerevisiae. The resulting NMR spectra were then analyzed by multivariate analysis, including principle component analysis (PCA) to identify differences in the spectra that can distinguish different mutants (Fig. 2). Two important results came out of these studies that would reveal the value of metabolomics in biological research. 

Dernovics, M. and Lobinski, R. Characterization of the selenocysteine-containing metabolome in selenium-rich yeast II on the reliability of the quantitative determination of selenocysteine. J. Anal. Atom. Spectrom. 2008, 23, 744-751. 

Cozzolino, D., Flood, L., Bellon, J., Gishen, M., De Barros Lopes, M. (2006) Combining near infrared spectroscopy and multivariate analysis as a tool to differentiate different strains of Saccharomyces cerevisiae a metabolomic study. Yeast, 23, 1089-1096. 

The size of the metabolome varies and depends on the species and type of organism. In the case of unicellular organisms such as baker s yeast (Saccharomy-ces cerevisiae), the number of metabolites amounts to 600, which is only a tenth of the number of genes (6000). In turn, plants are characterized by a much larger number of metabolites. The metabolome of Arabidopsis Arabidopsis sp.) is estimated to be 5000 compounds. In total, the number of metabolites of all plant species is estimated at 90,000-200,000 compounds, of which secondary metabolites make up a large proportion. 

There has been a growing application of metabolomics to wine yeast and fermentation as more people have recognized the power of these techniques. One application of metabolomics has been to study the interactions of yeast during fermentation. Howell et al. (2006) used metabolic profiling to study how multiple strains of Saccharomyces spp. grown together in grape juice affect the flavor and aroma compotmds in the fermented wine. 

Mashego, M., Van Gulik, W., and Heijnen, J. 2006. Metabolome dynamic responses of Saccharomyces cerevisiae to simultaneous rapid perturbations in external electron acceptor and electron donor. FEMS Yeast Res. 7(1), 48-66. 

We see two major appearing frontiers for new kinds of molecular data. The first is proteomics (See Chapter 4 of volume 2) and metabolomics. With a combination of 2D gel, mass spectrometry, protein microarray and yeast-two-hybrid methods, a large amount of protein sequence, expression, and interaction data will be produced on a cell-wide level. On the one hand, bioinformatics has to address the challenge of interpreting these data. On the other hand, especially the protein interaction data will provide an interesting basis for probing deeper into the details of regulatory networks. Such data are collected in special protein interaction databases such as DIP [9,10] and BIND [11],... 

Rossouw, D., Naes, T., Bauer, F. (2008). Linking gene regulation and the exo-metabolome a comparative transcriptomics approach to identify genes that impact the production of volatile aroma compounds in yeast. BMC Genomics, 9, 530. http //dx.doi.org/10.1186/1471-2164-9-530. 

Ewald JC, Heux S, Zamboni N (2009) High-throughput quantitative metabolomics workflow for cultivation, quenching, and analysis of yeast in a multiwell format. Anal Chem 81 3623-3629 Feist AM, Zielinski DC, Orth JD, ScheUenberger J, Herrgard MJ, Palsson BO (2010) Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli. MetabEng 12 173-186... 

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