Brewer's yeast strain optimisation may lead to a more efficient beer production process, better final quality or healthier beer. However, brewer's yeast genetic improvement is very challenging, especially true when it comes to lager brewer's yeast (Saccharomyces pastorianus) which contributes to 90% of the total beer market. This yeast is a genetic hybrid and allopolyploid. While early studies applying traditional genetic approaches encountered many problems, the development of rational metabolic engineering strategies successfully introduced many desired properties into brewer's yeast. Recently, the first genome sequence of a lager brewer's strain became available. This has opened the door for applying advanced omics technologies and facilitating inverse metabolic engineering strategies. The latter approach takes advantage of natural diversity and aims at identifying and transferring the crucial genetic information for an interesting phenotype. In this way, strains can be optimised by introducing "natural" mutations. However, even when it comes to self-cloned strains, severe concerns about genetically modified organisms used in the food and beverage industry are still a major hurdle for any commercialisation. Therefore, research efforts will aim at developing new sophisticated screening methods for the isolation of natural mutants with the desired properties which are based on the knowledge of genotype-phenotype linkage.

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-DNA microarray has been a useful tool for global-scale transcriptome analysis. To study the cellular response to expression of recombinant proteins, we compared the transcriptional profiles of recombinant Pichia pastoris strains overexpressing amylase and interleukin-2 versus that of the control strain at different cellular states. The microarray analysis was carried out via the use of Yeast_2 array specific for Saccharomyces cerevisiae and Schizosaccharomyces pombe. The transcirptome analysis of each studied strain at logarithmic growth phase and stationary growth phase showed hundreds of significant differences. In contrast, in comparison of studied strains at the same time points, the numbers of gene which are differentially expressed is rather low. Interestingly, the expression of heterologous alpha-factor secretion signal in the strains overexpressing amylase and interleukin-2 was up-regulated by more than 15 times and 140 times at the exponential and stationary phase, respectively. The results also provide evidence about the false positive result in microarray data when using non-specific array.

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