Linking gene regulation and the exo-metabolome: A comparative transcriptomics approach to identify genes that impact on the production of volatile aroma compounds in yeast
Institute for Wine Biotechnology, University of Stellenbosch, Stellenbosch, South Africa; Centre for Biospectroscopy and Data Modelling, NOFIMA FOOD, Matforsk AS, Oslovegen 1, 1430 Ås, Norway
Background: 'Omics' tools provide novel opportunities for system-wide analysis of complex cellular functions. Secondary metabolism is an example of a complex network of biochemical pathways, which, although well mapped from a biochemical point of view, is not well understood with regards to its physiological roles and genetic and biochemical regulation. Many of the metabolites produced by this network such as higher alcohols and esters are significant aroma impact compounds in fermentation products, and different yeast strains are known to produce highly divergent aroma profiles. Here, we investigated whether we can predict the impact of specific genes of known or unknown function on this metabolic network by combining whole transcriptome and partial exo-metabolome analysis. Results: For this purpose, the gene expression levels of five different industrial wine yeast strains that produce divergent aroma profiles were established at three different time points of alcoholic fermentation in synthetic wine must. A matrix of gene expression data was generated and integrated with the concentrations of volatile aroma compounds measured at the same time points. This relatively unbiased approach to the study of volatile aroma compounds enabled us to identify candidate genes for aroma profile modification. Five of these genes, namely YMR210W, BAT1, AAD10, AAD14 and ACS1 were selected for overexpression in commercial wine yeast, VIN13. Analysis of the data show a statistically significant correlation between the changes in the exo-metabome of the overexpressing strains and the changes that were predicted based on the unbiased alignment of transcriptomic and exo-metabolomic data. Conclusion: The data suggest that a comparative transcriptomics and metabolomics approach can be used to identify the metabolic impacts of the expression of individual genes in complex systems, and the amenability of transcriptomic data to direct applications of biotechnological relevance. © 2008 Rossouw et al; licensee BioMed Central Ltd.
fungal protein; protein AAD10; protein AAD14; protein acs1; protein bat1; protein YMR210W; transcriptome; unclassified drug; volatile organic compound; article; controlled study; fermentation; fungal genetics; fungal metabolism; fungal strain; gene control; gene expression; gene identification; gene overexpression; metabolomics; nonhuman; prediction; transcriptomics; wine; yeast; comparative study; DNA microarray; fungal gene; gene expression profiling; gene expression regulation; genetics; metabolism; metabolome; methodology; microbiology; multivariate analysis; odor; Saccharomyces cerevisiae; time; Fermentation; Gene Expression Profiling; Gene Expression Regulation, Fungal; Genes, Fungal; Industrial Microbiology; Metabolic Networks and Pathways; Metabolome; Metabolomics; Multivariate Analysis; Odors; Oligonucleotide Array Sequence Analysis; Saccharomyces cerevisiae; Time Factors; Volatile Organic Compounds; Wine