Proteasomes: The Machines of Life
Proteins carry out almost all of life's essential processes, often working in highly complex multicomponent assemblies that sometimes include other types of macromolecules such as DNA or RNA. These machines typically work together in functional networks called "pathways" that underlie the dynamic life of a cell as they execute important metabolic functions, mediate information flow within and among cells, and build cellular structures.
Breaking
down unneeded proteins — a task equal in importance to synthesizing new proteins
— is accomplished by the orderly action of several multiprotein complexes.
At the heart of this process is a multiprotein complex called the proteasome.
This is a fundamental kind of machine that has been highly conserved during
evolution. Some form of it is found in organisms ranging from simple bacteria
to humans. These machines of destruction consist of a tunnel-like core with
a cap at either or both ends (
see figure at right). The core is formed by four
stacked rings surrounding a central channel that acts as a degradation chamber.
The caps recognize and bind to proteins targeted by the cell for destruction,
then use chemical energy to unfold the proteins and inject them into the central
core, where they are broken into pieces. Specific proteins are targeted to enter
the proteasome by the action of yet another class of machine called E3 ligases.
One type of E3 ligase machine is called the SCF complex. It consists of at least
five kinds of proteins, and its job is to target and feed specific substrate
proteins to the proteasome. In organisms ranging from yeast to human, this class
of machines is responsible for chemically marking specific proteins for destruction
by attaching to them yet another protein called ubiquitin that functions as
a destruction tag. By using this multimachine pathway, cells can regulate and
execute the highly specific elimination of a few kinds of proteins, while leaving
the others intact. Such specific regulation of protein degradation gives cells
a way to regulate major dynamic changes and cellular "decisions."
A magnificent example is the central role of the proteasome pathway in causing
a cell to proceed with the decision to replicate itself. In yeast cells a critical
trigger for cell replication is degradation of Sic1, which is a protein that
inhibits the chemical activity of CDC28. CDC28 is a cyclin-dependent kinase
protein, and proteins like it are key regulators of the cell-division cycle
in organisms ranging from yeast to human. After eliminating the biochemical
Sic1 "brake" due to the action of SCF and the proteasome, the kinase
is then free to trigger progress toward DNA replication and associated events
of cell replication.
A very different kind of multiprotein complex forms in cells to transduce one important group of molecular signals from outside the cell. The immediate effect of this signal transduction is to change gene expression in the cell receiving the signal, which in turn causes the cell to behave differently after receiving the signal. For example, in yeast the transduction of one such signal causes the cell to cease dividing and begin the process of mating. At the heart of this signal transduction pathway are three different proteins of the MAP-kinase family that act upon each other in series in response to the signal. Recent discoveries show that they do not do this by "swimming" about the cell until they bump into each other entirely by chance, as was once thought. Instead the three kinases come together into an orderly structure by collectively binding to a protein "scaffold." In the pathway that mediates mating in yeast, this scaffold is a protein called STE5. The pathway cannot function properly without forming the STE5-mediated complex. Many different variations on the three-member MAPK cascade theme are used in all higher organisms to transduce a diverse set of specific signals. It is therefore likely that there is a correspondingly large family of multiprotein complexes of this basic machine type, and scientists would be greatly aided by knowing the composition of all such machines. A more-general implication is that other pathways featuring a series of sequential reactions may also exist in the cell as ordered multiprotein complexes, and this in turn could powerfully affect the way the pathways function, whether and if they engage in chemical "crosstalk," and how they are regulated. This is another critical reason for learning the composition of these machines.
An
entirely different class of molecular machines functions as motors, converting
chemical energy into mechanical motion, both linear and rotary. The dynein motor
(see figure at left), a cellular complex believed to be composed of 12 distinct
protein parts, performs fundamental transportation tasks critical to the cell;
defects in its structure can prove fatal. This machine converts chemical energy
stored in an ATP molecule into mechanical energy that moves material though
the cell along slender filaments called microtubules. One of the dynein motor's
most important functions occurs during cell division, when it helps move chromosomes
into proper position, as seen in the cell division image.
Multiprotein machines, such as the ones described above, tend to be quite highly conserved in overall composition and function during evolution albeit often as variant forms on a basic theme. As a result, one can expect that much of what is discovered in one organism will be applicable to others. Once a class of multiprotein machines is defined, variations on the theme can be plumbed to illuminate critical details for pathways of high relevance to DOE. No one yet knows the number of different basic types of such machines, but extrapolation from discoveries of the past few years, coupled with new knowledge of total protein diversity that comes from having whole-genome DNA sequences, suggests that the number is in the range of several thousand types. This suggests that the goal of characterizing the basic repertoire of machine types in the Genomics:GTL program is an audacious but tractable undertaking.
