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Ubiquitin and related molecules do more than just degrade and recycle cellular waste

The proteins of the ubiquitin family have long been regarded as cellular Post-its with “to be discarded” written on them. However, over the last ten years it has become increasingly clear that the proteins of the ubiquitin family that cells use to label defective or unneeded proteins also regulate a broad range of important cellular processes. It has also been found that they are involved in the pathogenesis of cancer and neurodegenerative diseases such as Parkinson’s disease. Dr. Andrea Pichler from the Max Planck Institute (MPI) of Immunobiology and Epigenetics in Freiburg and her group of researchers are investigating the regulation of the covalent attachment of ubiquitin and SUMO (small ubiquitin-related modifier) to their substrates and its effects on the biological level.

In 2004, Aaron Ciechanover, Avram Hershko and Irwin Rose were awarded the Nobel Prize in Chemistry for the discovery of ubiquitin-mediated protein degradation. Ubiquitin is a small protein that consists of 76 amino acids and performs a plethora of functions by conjugating to different proteins. The protein’s basic function is described here: Erroneously folded or unwanted proteins that are to be broken down are tagged with one or several ubiquitin molecules. This molecular label sends a signal to the cells’ waste disposal machinery (ed. note: proteasomes) that the proteins can be cut into small pieces and recycled.

Around 10 known ubiquitin representatives play a regulatory role in the majority of cellular signalling networks that is similar to the role played by enzymes that phosphorylate signalling molecules. “In addition to degrading proteins, ubiquitin and its relatives such as SUMO are involved in many cellular processes, including DNA repair, cell division and embryonic development,” said Dr. Andrea Pichler from the Max Planck Institute of Immunobiology and Epigenetics in Freiburg.

The photo shows nine people standing on a staircase.
Research group led by Dr. Andrea Pichler (at the back) from the Max Planck Institute (MPI) of Immunobiology and Epigenetics in Freiburg. © Dr. Andrea Pichler

Cellular regulators

The targeting of proteins for destruction or other cellular processes depends on whether an enzyme or signalling molecule is tagged with just one ubiquitin molecule or with a polyubiquitin chain. It is therefore of crucial importance to understand how ubiquitin molecules attach to specific target structures and how the cells can regulate this process. Three enzymes are involved in attaching ubiquitin molecules to larger proteins; the molecules are identified by the letter E and consecutive numbers (E1, E2, etc.). The ubiquitin-activating enzyme E1 catalyses the first step in the ubiquitination reaction; it binds to an ubiquitin molecule, activates it and passes it on to E2 (conjugation protein). E2 either passes the ubiquitin molecule directly on to a targeted substrate or complexes with an E3 molecule (ubiquitin protein ligase), which recognises that the protein is tagged and catalyses the transfer of ubiquitin to that protein.

The beauty of a smear: SUMO-modified cellular proteins form a typical smear in an electrophoresis gel. © Dr. Andrea Pichler

Hundreds of E3 enzymes are now known to catalyse the transfer of ubiquitin to target proteins; a handful of E3 enzymes are also known to catalyse the transfer of SUMO, which was discovered around two decades after ubiquitin. The E3 enzymes only share a few conserved structures, which makes them very specific - ubiquitin and SUMO are thus only transferred to specific proteins, and only interfere with specific cellular processes. “E3 seems to be a key regulator that cells use to define the specific effect of ubiquitin labelling,” said Pichler.

Despite the major importance of E3, Pichler and her team are more interested in the molecular basis of E2 enzyme regulation, as experiments and literature surveys have led them to an unexpected discovery. Whilst different studies correlate E2 upregulation with various types of cancer and neurodegenerative diseases, Pichler and her group of researchers have discovered that some E2 enzymes can also be tagged with SUMO.

What function does the process of E2 SUMOylation have? “We assume that cells are also able to interfere with the labelling of proteins with ubiquitin-related molecules on the level of E2 enzymes,” said Pichler. In contrast to the regulation of cellular processes on the E3 level where a large variety of E3 enzymes and their target structures enables the system to be finely adjusted, E2 appears to be more unspecific.

Regulatory role in reproduction

“It appears that the regulation of different signalling processes in cells by way of E2 occurs in a more general way,” said Pichler. “The modification of the quantity of E2 has immediate consequences for many different downstream cellular processes.” The Freiburg researchers hypothesise that diseases such as cancer are caused by the deregulation of hundreds of molecular regulators. They further assume that such diseases are, amongst other things, the result of E2 deregulation, which is expected to have widespread consequences on all downstream ubiquitination and SUMOylation events and hence interfere with a large number of signalling networks.

Pichler and her team’s experiments are therefore mainly focused on elucidating the question as to what consequences SUMOylation or E2 overexpression have on cellular processes. Pichler, who originally worked in the field of biochemistry, is trying to solve this question by focusing on the individual molecules involved in these processes and on how they interact. Where on E2 can a SUMO molecule attach? Does this modify its activity in relation to unmodified E2 enzymes? Which cellular proteins are no longer modified or modified to a much greater degree when an E2 enzyme is SUMOylated? One thing that Pichler and her team’s work has led to is the discovery that a SUMOylated E2 yeast enzyme plays a crucial role in meiosis. “The regulation of E2 by way of the post-translational attachment of SUMO plays a crucial role in sexual reproduction, and as such is an excellent example that confirms the crucial role of ubiquitin-related modifiers in biological processes,” said Pichler.

In another ongoing project carried out in cooperation with Dr. Klaus-Peter Knobeloch, a mouse geneticist in the Department of Neuropathology at Freiburg University, Pichler and her team are investigating the role of E2 in Alzheimer’s disease in the hope of eventually finding out how cells regulate crucial processes by way of ubiquitin and related modifiers. Detailed insights into the regulation of cellular processes by way of ubiquitination and SUMOylation might at some stage in the future enable researchers to interfere with deregulated signalling networks in cancer and neurodegenerative diseases and thus go some way towards restoring the proper function of cells.

Further information:
Dr. Andrea Pichler
Max Planck Institute of Immunobiology and Epigenetics

Stübeweg 51

79108 Freiburg

Tel.: +49 (0)761/ 5108 - 777
E-mail: pichler(at)immunbio.mpg.de

Website address: https://www.gesundheitsindustrie-bw.de/en/article/news/ubiquitin-and-related-molecules-do-more-than-just-degrade-and-recycle-cellular-waste