By David N. Leff
One Monday morning, a heavy-set assembly-line worker picks up a heavy wrench and bashes a car engine. His foreman surmises the man is still hung over from a weekend of binging.
The same sort of mayhem goes on inside every cell in your body. Cell biologist Jonathan Yewdell, at NIH¿s National Institute of Allergy and Infectious Diseases (NIAID), employs the same metaphor: ¿Inhibitors have been developed,¿ he observed, ¿for specifically inactivating proteasomes in the body. It¿s basically like taking a very large wrench and hitting an engine very hard. The cell is not particularly happy, and lots of things get screwed up, which tells you that the proteasome has been humming along all the time, at its job.
¿The proteasome is a very complicated structure,¿ Yewdell continued. ¿It¿s got a lot of different forms, and the most remarkable thing about it is that it¿s incredibly abundant. All of its components constitute fully 1 percent of a cell¿s proteins. That tells you right off that it¿s doing very important things. What it¿s doing is degrading all sorts of proteins that the cell no longer wants or needs.¿
At the University of T|bingen in Germany, immunologist Hans-Georg Rammensee has his own analogy for describing a proteasome: ¿It¿s a proteolytic enzyme that cuts proteins ¿ which are long chains of amino acids ¿ into pieces.¿ He pictures this complex protease as ¿like a barrel. Inside this barrel there are three enzymes at certain well-defined places. The protein marked for degradation enters the barrel at the top, and inside it¿s taken apart by three different double enzymes,¿ he told BioWorld Today.
In today¿s issue of Nature, dated April 13, 2000, Rammensee wrote of the proteasome¿s seemingly destructive activity: ¿Every production process, be it industrial or cellular, aims at high efficiency. To achieve this end, the management must choose between high output at the cost of high waste, or slow, precision manufacturing with minimal error.¿
Mammalian cells go for the fast lane, so protein production errors pile up just beyond the ribosome. This is the processing plant that converts free amino acids into proteins. The erroneous rejects are called DRiPs ¿ defective ribosomal products. They never grow up to become mature proteins, owing to mistakes when DNA translates genes into RNA, or misfolding of their molecular structure or other mishaps.
New Amino Acids For Old
Here¿s where the busy-beaver proteasomes take over, as quality-control enzymes that slice and dice the protein chains back into free amino acids for recycling into new proteins.
Rammensee¿s News & Views editorial in today¿s Nature, titled ¿Perfect use of imperfection,¿ comments on two proteasome-oriented research papers in the same issue. One, titled ¿Rapid degradation of a large fraction of newly synthesized proteins by proteasomes,¿ is jointly authored by Yewdell, who heads the Cellular Biology Section in NIAID¿s Laboratory of Viral Diseases, and Jack Bennink, chief of viral immunology in that lab.
The other article reports, ¿The major substrates for TAP in vivo are derived from newly synthesized proteins.¿ Its senior author is tumor biologist Jacques Neefjes, at the Netherlands Cancer Institute in Amsterdam.
TAP stands for ¿transporter associated with antigen processing.¿ It moves peptides ¿ notably those degraded from proteins by proteasomes ¿ from the cell¿s cytosol into its endoplasmic reticulum. From this organelle, which abuts the ribosome, antigenic fragments of discarded or invasive peptides are presented to the immune system¿s killer T cells for termination with extreme prejudice.
Acting as informant in this operation is a small, ubiquitous molecule, aptly called ubiquitin, which slaps a marker on every protein condemned to fragmentation by a proteasome.
From their prior discovery of DRiPs, and other data, Yewdell and his co-authors concluded that ¿the ribosome is not perfect. There¿s a certain level of inefficiency, and what we showed in this paper is that its number may be a lot higher than people think it is. Under the most normal circumstances, with the most normal cells, the number of proteins rejected during production seems to be around 30 percent.
¿But we found,¿ Yewdell told BioWorld Today, ¿that it can be as high as 80 percent or 90 percent under other, abnormal circumstances ¿ such as taking a cell line that¿s been cultured for 50 years. These are the immortalized HeLa cancer cells, which have accumulated lots of mutations and chromosomal breaks in their proteins. From our in vitro experiments with HeLa cells,¿ he said, ¿that¿s where we came up with the 80 percent number.¿
Moreover, he went on, ¿We wanted to show for a specific gene product that we could demonstrate these defective forms that didn¿t fold properly and are tagged for proteasome destruction by ubiquitin.¿ The co-authors chose the HIV¿s infective, nose-cone Gag protein, ¿which, by the way, is known to be a good target antigen for killer T cells,¿ and determined ¿that at least 30 percent of what¿s newly made of this protein seems to be rapidly degraded as well.¿
Yewdell observed, ¿The field has taken off in the last few years, and the major reason is the development of proteasome inhibitors. Cells treated with these inhibitors,¿ he pointed out, ¿usually die within 12 to 24 hours.¿
Potent Proteasome Inhibitor Seeks Medical Future
¿You would think,¿ Yewdell continued, ¿that such a powerful class of drugs could have no use clinically because they¿d be toxic. But apparently that¿s not true; there are even clinical trials that look very promising, using proteasome inhibitors for cancer or inflammation. (See BioWorld Today, Feb. 4, 1997, p. 1.)
Currently, the co-authors are ¿looking for these DRiPs in other viral proteins. We also have another paper submitted in which our first author, visiting scientist Ulrich Schubert, shows that for this HIV Gag protein, it appears that its defective form can interfere with the function of the normal forms and inhibit HIV replication.
¿This is also the target for the retroviral protease inhibitor,¿ Yewdell noted, ¿which is part of the multidrug therapy used by HIV-positive people.¿ He concluded, ¿It looks as if there may be another way to do this, which is to inhibit proteasomes.¿