Researchers from the Proteome Center at the University of Tübingen have identified a previously unknown form of ubiquitin, a regulatory protein that functions in numerous cellular processes, including inflammatory processes. Ubiquitin is known to contribute to disease development as well as help correct protein synthesis errors. It can form chains of several molecules attached to target proteins, a process that is referred to as polyubiquitylation.
Ubiquitin is a small protein found (ubiquitously) in all cells of eukaryotic organisms from plants to humans. Ubiquitin binds to other proteins and influences their fundamental properties. The modification of proteins by ubiquitin is of key importance for many intracellular regulatory processes. The discovery of this modification process, which is referred to as ubiquitylation, won the Nobel Prize for Chemistry in 2004. Ubiquitin is known to contribute to disease development as well as help correct protein synthesis errors. It can form chains of several molecules attached to target proteins, a process that is referred to as polyubiquitylation.
Researchers from the Proteome Center Tübingen (director Prof. Dr. Boris Macek) at the University of Tübingen have now identified a new form of polyubiquitylation that plays an important role in the regulation of inflammatory processes. The results of the researchers from Tübingen are part of a large international study that recently appeared in the journal Nature.
Boris Macek describes his group’s finding as follows: “Until now, two major forms of polyubiquitylation were known. In cooperation with Prof. Ivan Dikic from Frankfurt, we have now been able to identity a new form of polyubiquitin, namely linear ubiquitin.” Using mass spectrometry, a method that measures the masses of ionised molecules (e.g. proteins), the scientists were able to determine the intracellular levels of polyubiquitin. “We have shown that the intracellular levels of linear ubiquitylation are around 30 times lower than those of the major forms of ubiquitin. In addition, we have shown that NEMO, an important regulatory protein of the NF-kappaB signal transduction pathway, is modified by this new form of ubiquitylation.”
The international study focused on the development and function of linear ubiquitylation. The study has shown that an important cellular regulatory mechanism, the NF-kappaB signal transduction pathway, is regulated by this new form of ubiquitylation. As the regulatory mechanism is involved in inflammatory processes, the researchers hope that the new insights may lead to the development of new therapies. “Detecting linear ubiquitin was a big challenge because the different forms of ubiquitylation are very difficult to tell apart. Actually, this is only made possible by mass spectrometry,” said Dr. Mirita Franz-Wachtel who was also involved in the study. “Due to the very small intracellular levels of this modification, it was necessary to apply the most sensitive biochemical methods and devices. Luckily, everything went well and we were able to confirm the biological findings of Prof. Dikic.”
The Proteome Center Tübingen was founded in 2003 by Prof. Alfred Nordheim as part of the Interfaculty Institute for Cell Biology. Since December 2008, the PCT has been led by Dr. Boris Macek, who is a junior professor for quantitative proteomics at the Faculty of Biology of the University of Tübingen. The PCT develops and applies state-of-the-art methods in quantitative mass spectrometry and proteomics. Proteomics is the study of all proteins of a cell or organism. In addition, as a Core Facility of the University of Tübingen, the PCT provides proteomics services to a broad scientific community. The PCT recently received funding totalling 720,000 euros from the German Research Foundation (DFG) and the Baden-Württemberg government for the purchase of a new-generation mass spectrometer
Reference: Fumiyo Ikeda, Yonathan Lissanu Deribe, Sigrid S. Skanland, Benjamin Stieglitz, Caroline Grabbe, Mirita Franz-Wachtel, Sjoerd J. L. van Wijk, Panchali Goswami, Vanja Nagy, Janos Terzic, Fuminori Tokunaga, Ariadne Androulidaki, Tomoko Nakagawa, Manolis Pasparakis, Kazuhiro Iwai, John P. Sundberg, Liliana Schaefer, Katrin Rittinger, Boris Macek und Ivan Dikic: SHARPIN forms a linear ubiquitin ligase complex regulating NF-kappaB activity and apoptosis. Nature 471:637-641, published 31st March 2011 (doi:10.1038/nature09814).