Certain protein degradation complexes, molecular “shredders”, dispose protein garbage. Molecular machines of that kind belong to the area of expertise of Eilika Weber-Ban, who together with her team has now successfully decoded how proteins in tuberculosis bacteria are prepared for disposal.
The fact that bacteria also possess a special “small” protein that can be attached to other proteins to alter their fate became known only recently. The “small” protein, which has been named “Pup”, helps to dispose of other proteins. However, its attachment may also control and regulate other important processes in the cells. “Pup” acts as a kind of marker. By being attached to another protein, it signals to the degradation complex that the marked protein is ready for disposal.
Mode of operation investigated in the test tube
Eilika Weber-Ban, research group leader at the Institute of Molecular Biology & Biophysics of ETH Zurich, and her team have now succeeded in understanding how the “Pup” protein works in the tuberculosis pathogen Mycobacterium tuberculosis. In the test tube, the researchers were able to show how Pup is attached to proteins. By doing so, the scientists discovered a new enzyme which they call “Dop”. The results were published recently in Nature Structural & Molecular Biology. The study may provide the basis for therapeutic strategies for people suffering from tuberculosis, especially in the case of patients in whom the pathogen has acquired resistance to antibiotics.
Coupling in two steps
The “Pup” degradation signal is coupled to a protein in two steps: first, “Dop” modifies the degradation signal to allow another enzyme to couple the modified “Pup” to its target protein. Now, the “molecular shredders” come into play: due to the attached Pup-signal the protein is ready to enter the “shredders”. These consist of a protein complex, which can be divided into two parts according to their function. Weber-Ban describes the entrance region, where the marked proteins enter through pores into the protease complex, as the engine. “Its task is to unroll the folded protein, which can be thought of as a ball of yarn, so it can be threaded into the second part of the shredder and chopped into pieces”, Weber-Ban explains. This function is carried out by molecular “scissors” inside the shredder.
In the eighties, scientists discovered a similar marker protein that disposes proteins in cells of multi-cellular organisms such as plants, animals and humans. The scientists were awarded the 2004 Nobel Prize for Chemistry for their discovery. However, until late 2008 it was unknown that proteins of that kind also existed in bacteria. According to the ETH researchers, however, the bacterial and human marker proteins differ markedly in their structure and in the way they function although they both ensure the degradation of proteins in cells.
It is still unclear which molecular processes are affected by “Pup”-mediated degradation in the tuberculosis pathogen. However, it is known that bacteria without this complex degradation mechanism cannot survive in the epithelial cells of the lungs. “This is why both the marker proteins and the degradation complex are suitable targets for therapy strategies”, says Weber-Ban. She points out that the marking system is a particularly good target in this respect, as it differs from that of humans and therefore drugs targeting the bacterial Pup-system should have no side-effects for humans.
- Striebel et al. Bacterial ubiquitin-like modifier Pup is deamidated and conjugated to substrates by distinct but homologous enzymes. Nature Structural & Molecular Biology, 2009; 16 (6): 647 DOI: 10.1038/nsmb.1597
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