February 12, 2001
Genome Wonderland Gives Way to Daunting Challenges of the Proteome
With the prodigious task of sequencing the human genome largely
behind them, researchers now face the more daunting challenge of
understanding the proteome—all of the proteins expressed in a
cell, according to Howard Hughes Medical Institute investigator Stanley
Fields.
In an article titled, "Proteomics in Genomeland" in the February 16,
2001, issue of the journal Science, Fields writes, "In the
wonderland of complete sequences, there is much that genomics cannot
do, and so the future belongs to proteomics, the analysis of complete
complements of proteins."
“These technologies must be made widely available so that no community of biologists feels disenfranchised. At least some biologists see the genomics and proteomics revolution as a real threat, and widespread availability of reagents and equipment will help alleviate that concern.”
Stanley Fields
Protein analysis, says Fields, is more complicated than figuring out
the linear sequence of DNA genes because researchers must carry their
analysis much further. "Proteomics includes not only the identifying
and quantifying of proteins, but also determining their localization,
modifications, interactions, activities, and, ultimately, defining
their function," wrote Fields, who is at the University of Washington.
Unlike DNA, proteins undergo complex biochemical modifications. A
single gene, for example, can encode multiple proteins by means of
alternative splicing of the messenger RNA. "All of these possibilities
result in a proteome estimated to be an order of magnitude more complex
than the genome," wrote Fields.
In an interview about the Science article, Fields cautioned
that scientists contemplating proteomics experiments will face major
challenges as they learn new laboratory techniques and establish
productive research collaborations. However, he expressed confidence
that agencies that fund research are up to the task of fostering the
necessary technologies and research infrastructure.
While researchers have gained a better understanding of thousands of
proteins based on studies of their biological activity in the cell,
Fields says that the huge number of proteins whose function is unknown
provides a daunting challenge. Assigning roles to these proteins
demands a new style of experimentation that "does not replace, but will
increasingly operate in company with, the traditional way biology has
been done," wrote Fields.
Fortunately, new technologies are enabling this work to proceed
rapidly. For example, identifying small networks of proteins that work
together has been aided by powerful analytical techniques such as mass
spectrometry—which sorts and identifies molecules based on their
mass. And sophisticated genetic analyses using yeast are pinpointing
associations between proteins, which can yield important clues about
protein function. New biochemical tagging techniques have greatly aided
attempts to determine the cellular location of proteins. Likewise,
computer algorithms are being used to analyze protein sequences to try
to identify proteins that have evolved together and thus are likely to
act in the same cellular process, according to Fields.
The next major advances in proteomics, says Fields, will be
technologies that measure how protein levels change dynamically during
cell processes. Techniques of mass spectrometry analysis of complex
protein mixtures "may allow human tissues to be used as the protein
source and makes feasible the discovery of early disease markers by
comparing the protein content of pathogenic cells with that of their
normal counterparts," wrote Fields. He also cited protein arrays of
tagged molecules as promising tools for exploring protein activity and
function.
"For a field so laden with razzmatazz methods, it is striking that
the number one need of proteomics may be new technology," wrote Fields.
He cited, in particular, the need for streamlined assays to automate
analysis of massive numbers of proteins. He also emphasized the need
for widespread distribution of proteomic technologies. "Only when every
laboratory is comfortable doing proteomics will its power be exploited
fully," he wrote.
In an interview, Fields added that "these technologies must be made
widely available so that no community of biologists feels
disenfranchised. At least some biologists see the genomics and
proteomics revolution as a real threat, and widespread availability of
reagents and equipment will help alleviate that concern."
Also, he said, many issues remain unresolved about how to organize
interdisciplinary collaborations required for advances in proteomics.
"How do you get computer scientists to work with protein chemists to
work with geneticists to work with combinatorial chemists, and so on?"
he asked. "I don’t think that has been sorted out at all."
While plans to create interdisciplinary proteomics centers "have
tremendous potential, it's not something that happens magically just
because you put different types of scientists together," he said. Thus,
he cautioned, "these kinds of interdisciplinary campuses, institutes,
or buildings have the potential to be fantastic but also the potential
to be unsatisfying. The scientists must speak a common language and
develop problems that they all want to work on."
Proteomics will also change the scale of biological research, said
Fields. "It is a major challenge to take scientists who are trained in
a traditional approach to biological research of small laboratories and
small-scale biology and introduce them to technologies that are
extremely powerful, but often expensive and centered in proteomics
centers or large laboratories," he said.
However, Fields said that he believes that federal funding agencies
and foundations are "increasingly aware of the complexities, the
problems, the need for technologies, and the funding to meet all these
challenges."
Fields emphasized that the massive proteomics effort will be well
worth it, because basic discoveries about the cell's protein machinery
will likely yield rapid clinical applications.
"My guess is that the timeframe for a new proteomic-based diagnostic
or treatment to go from the academic laboratory to prototype to
engineering to commercial application will be rapid and will continue
to shrink," he said.
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