Biology Reference
In-Depth Information
alter flux through a particular desired pathway
[6]
. It has
also been recognized that the few genes that do have the
ability to alter metabolic flux can often to alter the flux of
many diverse cellular pathways
[6]
. Formally, a biological
network can be described where 'nodes' represent genes,
and two genes are connected by an 'edge' if both are, for
example, members of the same metabolic pathway. 'Hubs'
are nodes that are highly connected, i.e., are connected to
many other 'nodes' or genes. If the network has a few hubs
yet most nodes are connected to few other nodes, the
topology is characteristic of a 'scale-free' network. Meta-
bolic flux and several other biological networks (e.g.,
genetic or protein interaction networks) are examples of
scale-free networks. This topology is responsible for the
perturbational robustness of the cell as a system. Thus,
perturbations of most genes (individually) may have
surprisingly few effects, while those that target hub genes
may dramatically alter the cellular response (see Chapter 9
for details).
approach had long been appreciated in the physical
sciences, it was new to biology, and the YGP set an
important model for future projects. In 1989, Goffeau built
a European consortium of 35 laboratories; that, although
not an easy task, was facilitated by the history of the tight-
knit S. cerevisiae community. At the end of the YGP 92
laboratories worldwide were active participants, repre-
senting the largest collaborative sequencing effort to date.
The YGP had a significant impact on the genome
sequencing projects that followed, all having adopted
similar combined-force strategies. The completion of the
YGP in 1996
[7]
revealed more than just DNA sequence:
the most significant revelation was that, despite decades of
effort, most of the protein-coding genes predicted from the
DNA sequence did not correspond to any that had previ-
ously been encountered
[8]
. Moreover, 35% of the genes in
the genome were designated orphan genes, that is homologs
of these genes had also escaped detection in other organ-
isms. These findings highlighted the importance of the full
yeast genome sequence, particularly in light of the fact that
by the end of the 1980s the gene discoveries were mostly
rediscoveries, suggesting that the genome had been tapped
out, when in fact the majority of the genes in the genome
had not yet been identified.
Yeast: A Pioneer and Driver of All Things
'Omic'
At the end of every sequencing project, the daunting task
of translating gene sequence into gene function presents
itself. As the first eukaryotic organism sequenced, and
equipped with a powerful arsenal of genetic and genomic
tools, S. cerevisiae has served as a gold-standard model
organism for functional annotation of gene sequences, and
has provided essential templates for the development of
nearly all things 'omic'.
The Yeast Deletion Project
Soon after the completion of the YGP the need to translate
sequence into function loomed. One of the most effective
approaches to elucidate gene function is to knock down or
knock out the activity of a gene and observe the effect on
the ability of the cell to function. Owing to the powerful
and unique genetic tools available to yeast, constructing
a gene deletion is straightforward and allows for a 'clean'
site-specific start-to-stop replacement of the wild-type
gene with a double-stranded laboratory-built DNA
knockout cassette module
[9]
. The painstaking task of
deleting and validating each of the ~6000 yeast genes one
at a time inspired the creation of a second consortium, the
Yeast Deletion Project (YDP)
[10,11]
. This effort,
involving 16 laboratories worldwide and championed by
the yeast geneticists Ron Davis (Stanford University) and
Mark Johnson (Washington University), allowed the
systematic construction of a genome-wide set of yeast
deletion strains, indisputably the most powerful functional
genomics tool available to date. Moreover, the results of
the YGP had made clear that the standard genetic
approaches were biased, yet few laboratories were inter-
ested in embarking on studies of orphan genes, because
without a new toolkit they were unlikely to uncover any
new biological insights. Thus the YDP served to remove
this bias, by allowing all genes to be studied simulta-
neously with nearly the same effort as that required for the
study of a single gene.
The Yeast Genome Project
The bold idea to sequence the S. cerevisiae genome was
formulated in 1986 by Andrew Goffeau (Universit
ยด
catholique de Louvain). At the time, the S. cerevisiae
sequencing project (YGP) paralleled challenges similar
in scope and scale to those faced by the HGP ~14 years
later. In many key ways the YGP set the stage for the
HGP; at the time, the S. cerevisiae genome was ~60
times the size of any previous sequencing effort,
compared to the HGP which was ~10 times larger than
all previous sequencing efforts combined. In addition,
both projects were subject to public scrutiny, and many in
the scientific community deemed the projects unjustifi-
able, owing to the enormous costs that many assumed
would result in little biological value, and which would
short-change hypothesis-driven science conducted in
individual laboratories.
From the start, Goffeau, together with Steve Oliver
(University of Manchester Institute of Science and Tech-
nology), appreciated that the magnitude of the YGP would
require a consortium effort. Although this 'big science'
