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Australasian Biotechnology (backfiles)
AusBiotech
ISSN: 1036-7128
Vol. 6, Num. 3, 1996
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Australasian Biotechnology,
Volume 6 Number 3, May/June 1996,pp.178-180
APAF : the Australian Proteome Analysis Facility
By Keith L Williams,
Macquarie University Centre for Analytical Biotechnology
(MUCAB) and
Bradley J. Walsh,
Australian Proteome Analysis Facility (APAF), School of
Biological Sciences, Macquarie University, Sydney, NSW,
Australia 2109. ph 61-2-98508212, fax 61-2-98508174 email
keith.williams@mq.edu.au
Code Number: AU96005
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Technological developments in protein science, combined with
ready access to DNA sequence databases and bioinformatics have
opened up a new field in biology: Proteome studies. The
federal Australian government has funded APAF as a major
national facility for Proteome analysis. This article
outlines the origins of APAF and how it is expected to impact
on Australian science and particularly biotechnology.
Introduction
The combination of two dimensional gel electrophoresis using
immobilised pH gradients, preparative loading (mg
protein/gel), and new microanalytical techniques have
revolutionised protein science to such an extent that the new
field of Proteome research is emerging. It is not surprising
that Australia is strongly represented in this new field as
there is a long tradition of protein chemistry in this
country. Indeed the first protein sequencer was built and
operated by Pehr Edman and Geoff Begg in Melbourne. There is
however a Swiss connection to the inception of APAF. In
Spring of 1993 Denis Hochstrasser from the Medical Hospital in
Geneva visited Sydney. Denis laboratory is at the forefront
of 2D-gel technology and he had solved the two key problems
which had held back the field for two decades. These were the
ability to make highly reproducible 2D-maps and being able to
load sufficient protein so that individual proteins purified
by the 2D-gel separation could be studied chemically
(Bjellqvist et al.1993). There remained however the problem
of how to study the proteins. Denis had thousands of pure
protein spots but each protein sequencer, the traditional
means by which proteins are identified, has the capacity of
studying perhaps 10 proteins in a week. Wherever he went
Denis spoke with protein sequencing laboratories to get some
of his samples studied. When Denis visited MUCAB and outlined
this dilemma, we decided that there must be a quicker and
cheaper way, and so research in the MUCAB laboratories began
to focus on this. Three years later we have a suite of new
instruments and the capacity not only to identify proteins,
but also to study their post-translational modifications.
The politics of major national facilities
When the APAF application was finally submitted, a colleague
who had been involved in a recent CRC application said to me
"now the work begins!". How right he was. Money is always
tight and with the prospect of perhaps half a dozen $10
million facilities, the competition was interesting. APAF had
the advantage of being very new, hence it fitted the
innovative concept of the major facilities program. On the
other hand being at the leading edge of a technology also
involves some risk, and so some thought it better to stay with
well established technolgies that had a proven track record
internationally. Fortunately, we had extremely strong support
from our international scientific colleagues as well as from
both local and international equipment manufacturers. At the
end of the day the decision was political and we (and several
others) benefitted at the expense of a major expediture on the
European Southern Observatory's very large telescope in Chile
(Swinbanks 1995). The outcome for the biological sciences
community was excellent, with $10 million being made available
for the establishment of AGRF (Australian Genome Research
Facility) and $7 million for establishing APAF (Australian
Proteome Analysis Facility).
How APAF is structured
The Major National Facilities funding is for the physical
aspects of the facility only, ie bricks and mortar and
equipment. We are left with the issue of funding the staff
and consumables. A strategy must also be developed to allow
renewal of the facility as new instruments become available.
This is a major challenge as the pace of change in this
emerging technology is such that investment in equipment in
1996 is unlikely to remain state of the art beyond 3-5 years
at most. In our application we envisaged that this would be
done by partnering with industry in research and development
of the next generation of Proteome technology. Currently we
are discussing partnerships with a number of companies
involved with 2D gel technology, HPLC, glycobiology, mass
spectrometry and robotics.
The operation of APAF will be under the guidance of a board
which will have the brief of providing strategic advice. In
the planning stage this will involve decisions about how
quickly projects can be started and the balance of short term
vs long term goals. APAF can start immediately in a labour
intensive fashion, but we must also invest some effort in
automating our technologies so that large scale projects can
be initiated.
What will APAF do?
While DNA genome sequencing is a major undertaking that is
unlikely to be completed on more than a small group of
eukaryotic organisms, the proteins of hundreds or even
thousands of organisms can be readily displayed using 2D gel
technology. Hence the way is open for Proteome studies on any
organism or tissue. Since a subcellular fraction, cell type,
or tissue can be displayed on a 2D gel, it is possible to get
a complete picture of both normal and diseased states. The
implications for both basic research and biotechnological
applications are major.
The components of Proteome research are the technology for
protein separation (using 2D gels), protein identification and
the means to study post-translational modifications to the
proteins, all at the level of a single 2D gel spot (ie at mg
amounts of protein). We have reviewed these advances recently
(Wilkins et al. 1995). Our approach to Proteome research is
to use a hierarchy of techniques such that many proteins are
screened quickly and cheaply, followed by more intensive (and
expensive) work on a small group of proteins of special
interest. Therefore, Proteome studies can be viewed as a
sequence of stepwise operations.
Relationship to the Australian scientific community
APAF is a national facility, hence it is owned by the national
community. It is our intention that access to APAF be as wide
as possible. Rather than sending samples to be processed, we
anticipate that many researchers will send someone from their
laboratory (or even come themselves) to be involved with the
Proteome processing. We are discussing with Macquarie
University affordable accommodation for visitors to the
facility. This will take a little while to organise, but we
expect many visitors to the facility to partake of our high
level training courses or to pursue projects.
The research centres which underpin APAF will have a major
influence on how it develops. In particular, MUCAB (Macquarie
University Centre for Analytical Biotechnology) will continue
research programs to provide the new technologies which APAF
will adopt. Precedents for this are already apparent from
several research projects that have had commercial outcomes.
For example APAF will use the GBC Scientific Equipment
"AminoMate" for amino acid analysis, the Beckman Instruments
"GlycoSite" for glycosylation site identification and the
Gradipore Ltd "Gradiflow" for protein prefractionation and
concentration. MUCAB had a role in the development of all
three instruments.
Ultimately Australia's role in the development of the new
field of Proteome research will be influenced by the success
of APAF, but all protein researchers around the country have a
role to play. We anticipate that many researchers will choose
to participate in these exciting times by conducting projects
in the new facility.
International linkages
An advantage of designating a national facility is that it
enables high level interactions with other countries. There
is much to be done in this area, but already discussions are
well in hand for making the facility a mirror site for the
Swiss ExPaSy database system. Discussions are also going on
with Adrian Gibbs (RSBS, ANU) and Professor Gojobori who heads
the DDBJ national database in Japan. As well as forging links
with databases these connections are already having concrete
outcomes.
For example, the close interactions with the Swiss
laboratories is not only productive in the area of basic
research, but also in database strcuture and searching.
Recent modifications to ExPaSy simplify the means of
identifying proteins by being able to search on a string of
different parameters (eg amino acid composition, pI, MW,
N-terminal sequence tag) and this has been driven by
collaborative work between MUCAB and Switzerland.
We are setting up structures around which the vitality of the
facility can be maintained, while at the same time supporting
efficient execution of national proteome projects. There is
much planning to be done and we welcome input from all
stakeholders in the scientific and business community (email
keith.williams@mq.edu.au).
References
Bjellqvist,B., Sanchez, J-C., Pasquali, C., Ravier, F.,
Paquet, N., Frutiger, S., Hughes, G.J. and Hochstrasser, D.F.
(1993b). Micropreparative 2-D electrophoresis allowing the
separation of milligram amounts of proteins.
Electrophoresis 14.1375-1378
Swinbanks,D. 1995. Australia backs innovation, shuns
telescope. Nature 378:653
Wilkins, M.R., Sanchez, J-C., Gooley, A.A., Appel, R.D.,
Humphery-Smith, I., Hochstrasser, D.F. & Williams, K.L.
(1995). Progress with proteome projects: why all proteins
expressed by a genome should be identified and how to do
it. Biotechnol. Genet. Eng. Rev.. 13:19-50.
Copyright 1996 Australian Biotechnology Association Ltd.
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