From radioactive probes to chromosome-sized DNA separated by

From the very beginning of brewing history, it was known
that lager yeast was different from other types. The first noticeable difference
was that brewing yeast strains did not produce any meiotic offspring. Today, we
know that a hybrid was formed from S.
cerevisiae and is now closely related Saccharomyces
species. Of all the genes researched, two of them appeared almost constantly. One
showed a hybridization pattern identical to that found in the corresponding S. cerevisiae gene, while the other
showed diversity. The finding of these two genes suggests that lager yeast
contains two types of chromosomes Sc- and Non-Sc- types. The chromosomes
derived from lager brewing yeast fell in one of the three categories homologous
— two chromosomes, one of paternal
origin, the other of maternal origin — chromosomes, which recombined normally
with S. cerevisiae chromosomes, homoeologous–same genetic constitution– chromosomes,
which rarely recombined with S. cerevisiae chromosomes, and mosaic –many
different combinations– chromosomes that were composed of homologous and
homoeologous segments.

The hybrid nature of lager brewing yeast has also been confirmed
by hybridization of radioactive probes to chromosome-sized DNA separated by
pulsed-field electrophoresis (Casey 1986b; Tamai et al. 1998; Yamagishi and
Ogata 1999). Experiments indicated at an early point that the lager brewing
yeast Sc-type of any given gene is identical to the corresponding S. cerevisiae
gene (Holmberg 1982; Nilsson-Tillgren et al. 1986; Petersen et al. 1987). The
complicated genetic nature of lager brewing yeast makes it difficult to the
breeding process. The deficiency in production of offspring would seem to
destroy classical breeding efforts. However, in the early 1980s, a method to
select for the few viable spores formed by lager brewing yeast and to
reconstruct functional brewing yeast from such offspring was devised (Gjermansen
and Sigsgaard 1981). Such spores could be used to form a heterogeneous
population for potential brewing strains, but these strains (Johannesen and
Hansen 2002; Hansen et al. 2002; Hansen and Kielland-Brandt 1996, 1996b;
Nilsson-Tillgren et al. 1986; Petersen et al. 1987) could be used for the
selection of recessive mutants (Gjermansen 1983). Out of many, none of the
techniques of analyzing genomes has been found, however times are changing.
With a rapid increase in DNA sequencing technology, such projects are now
achievable. The whole genome sequence of one strain of lager brewing yeast has
been obtained. A combination of different kinds of sequencing were used to
perform a total of 348,001 sequence reads of the genome of lager brewing yeast.
This sequence also consists of 160 million base pair of DNA. The sequences were
assembled into contigs. It was found that lager brewing yeast’s genome was 23.2
million base pairs, which is twice the size of S. cerevisiae genome
(Saccharomyces Genome Database; SGD). Contigs are classified into two groups
those with DNA and those with identities around 85%. It is now evident that two
yeast species came together to make a lager brewing yeast hybrid. One of these
ORFs (Open Reading Frame) has reported a gene consisting of a specific fructose
(Gonçalves et al. 2000). Fructose transport is one of the markers tha
distinguish S. pastorianus and S. bayanus from other Sacchromyces sensu stricto
species (Rodrigues de Sousa et al.

1995). S. bayanus is generally isolated
from oenological environments, rich in fructose. Although this sugar does not
play a major role in brewing, the gene for has stayed around in the lager
brewing yeast. In contrast to the protein-encoding regions, the non-Sc-type
intergenic regionsin the lager brewing yeast are diverged from the Sc-type. In
fact, such differential expression of homoeologues in lager brewing yeast has
been reported for the BAP2 gene (encoding a branchedchain amino acid permease)
homoeologues (Kodama et al. 2001), and for MET2 (encoding homoserine O-acetyl
transferase) and MET14 (encoding adenosylphosphosulphate kinase) (Johannesen
and Hansen 2002). “These findings tell us that the lager brewing yeast is not a
polyploid with two divergent but similarly functioning genome parts, but is in
fact a unique organism with a biological complexity larger than any of the
species that took part in its formation.” (Panoutsopoulou et al. 2001; Olesen
et al. 2002; James et al. 2003). In addition an expression analysis during beer
fermentation using signature sequencing has been performed. More than 1400
genomes have been tested and almost half of them showed a different gene expression.
In order to study this gene difference, DNA arrays containing lager brewing
yeast have been tested (Nakao Y, Kodama Y, Fujimura T, Nakamura N, and Ashikari
T). The size of DNA molecule was a little smaller than that of S. cerevisiae,
but the same as S. pastorianus .Also the gene order of lager DNA is different
from S. cerevisiae but the same as S. bayanus. Moreover, with the introduction
of RNA analysis, genes of lager brewing yeast are different from those of S.
cerevisiae (Foury et al. 1998). These results tell us that lager brewing yeast
got its mitochondrial genome from a non-S. cerevisiae ancestor, thus containing
two different nuclear genomes.

            As
mentioned before the mosaic structure of lager brewing yeast chromosomes has
been discovered a long time ago. The number of recombination events, however,
has not been discovered, not to mention combinational points. Such information
is required to establish the optimal strategies for targeted molecular
breeding. These answers have been answered through analysis of the sequence
contigs obtained by the lager brewing yeast whole genome sequence analysis, as
described before, and partly by hybridization experiments with S. cerevisiae