Application of Shotgun DNA Microarray Technology to Gene Expression Analysis in Lager Yeast

We used a shotgun DNA microarray strategy for gene expression analysis in brewing lager yeast for the first time. We constructed a random genomic library from a bottom-fermenting (lager) yeast strain, Weihenstephan 34/70, which is widely used in lager beer brewing. A DNA fragment size of ≈2.5 kbp was chosen, and 20,160 clones from the genomic library were printed on the shotgun DNA microarray. The gene expression analysis was carried out with total RNA extracted from lager yeast strains for a series of fermentation trials. Among the 7,636 spots that showed more than the limit of detection, 207 were selected as showing significant expression changes. In all, 37 spots were first repressed and then induced, and 62 spots were first induced and then repressed. Those spots were sequenced, annotated, and categorized into four clusters composed of the following sets of genes: 1) significantly induced, 2) significantly repressed, 3) first repressed and then induced, and 4) first induced and then repressed. These different patterns of expression for genes related to the fermentation process have been discussed. Therefore, we have shown that the shotgun DNA microarray technology is a very useful tool for accomplishing gene expression studies with lager yeast strains.