Novel form of ubiquitin protein characterized: New insights into inflammation and cell death

Ubiquitin, a small protein present in cells of higher organisms, binds to other proteins and influences their fundamental properties. Modification of proteins by ubiquitin -the so-called ubiquitylation- is of greatest importance in many regulatory processes in the cell and its discovery was awarded the Nobel Prize in 2004. Ubiquitin can form chains consisting of several molecules attached to a target protein to form polyubiquitylation. Among other functions, this form of ubiquitylation regulates protein levels and its deregulation can lead to various disorders.

Researchers from the Proteome Center Tuebingen (PCT) have characterized a novel form of polyubiquitylation that plays an important role in inflammation processes and cell death. Their results are a part of a large international study led by Prof. Ivan Dikic from the University of Frankfurt and appear in the journal Nature.

Prof. Boris Macek, Director of the PCT, describes the finding: "Until now, two major forms of polyubiquitylation were known. Our collaboration with Prof. Dikic has revealed the existence of a novel form of polyubiquitin -- the "linear" ubiquitin." Using mass spectrometry, a method that can measure the masses of ionized molecules (e.g. proteins) scientists were able to determine the intracellular levels of this new modification. "We showed that the intracellular levels of the linear ubiquitylation are about 30 times lower than that of the major forms of ubiquitin. In addition, we showed that NEMO, an important regulatory protein of the NF-kappaB signal transduction pathway, is modified by this new form of ubiquitylation."

The topic of the study was the biosynthesis and function of linear ubiquitylation. The results have shown that an important cellular regulatory mechanism, the NF-kappaB signal transduction pathway, is regulated by this new form of ubiquitylation. This regulatory mechanism is involved in inflammation processes and the scientists hope that the new insights into its regulation may lead to development of new therapies.

„It was a big challenge to detect linear ubiquitin, because different forms of ubiquitylation are very difficult to tell apart and this is actually only possible by mass spectrometry," says Dr. Mirita Franz-Wachtel, who also participated in the study. "Due to very small intracellular amounts of this modification we had to apply the most sensitive biochemical methods and instrumentation. Luckily, everything went well and we could fully confirm the biological findings of Prof. Dikic"

The Proteome Center Tuebingen was founded as a part of the Interfaculty Institute for Cell Biology in 2003 by Prof. Alfred Nordheim. Since December 2008 the PCT is led by Dr. Boris Macek, who is a Junior (Assistant) Professor for Quantitative Proteomics at the Faculty of Biology of the University of Tuebingen. The PCT develops and applies the modern methodologies in quantitative mass spectrometry and proteomics, which is the study of the complete protein complement of the cell or organism. In addition, as a Core Facility of the University of Tuebingen, the PCT provides proteomics service to a broad scientific community. The PCT has recently received funding of 720,000 EUR from the DFG and MWK BW for a purchase of a new-generation mass spectrometer.