La reconnaissance des chaînes NEDD8 et leur signalisation

par Igor Meszka

Projet de thèse en Biologie Santé

Sous la direction de Dimitris Xirodimas.

Thèses en préparation à Montpellier , dans le cadre de Sciences Chimiques et Biologiques pour la Santé (Montpellier ; Ecole Doctorale ; 2015-....) , en partenariat avec CRBM - Centre de Recherche en Biologie cellulaire de Montpellier (laboratoire) et de Protéines de la famille ubiquitine et regulation de la croissance cellulaire (equipe de recherche) depuis le 01-10-2018 .

  • Titre traduit

    The recognition and signalling of NEDD8 chains

  • Résumé

    UbiCODE Project Understanding how organisms respond to environmental stress has critical implications both on quality of life and treatment of diseases. Our general research interest is to understand the cellular response to environmental stress, which cause DNA (genotoxic stress) or proteins (proteotoxic stress) damage. Organisms have developed a series of sophisticated processes to detect and repair such damages. In cases where the damage cannot be repaired mechanism ensure the elimination of unrepaired DNA (apoptosis) or unrepaired proteins (degradation). A family of small proteins called the family of ubiquitin molecules (Ubls), play a critical role in all above-described aspects of the response to stress. Defects in components of the ubiquitin family are often found in pathologic conditions including cancer and neurodegenerative diseases. It is therefore not a surprise that this family of proteins represents major targets for therapeutic intervention. Understanding how the ubiquitin family is involved in the cellular response to stress has important implications both for fundamental research and at the social-economic level. Ubiquitin controls protein function by modifying targets as single molecule. In addition, ubiquitin makes polymeric chains by modifying other ubiquitin molecules on 8 specific amino acids. Depending on which amino acid is used a different type of chain is created with distinct biological functions. This is because each distinct ubiquitin chain is recognised by cellular factors (receptors) that initiate a signalling event. For example, ubiquitin chain formation through Lysine11 and/or Lysine48 targets substrates for proteasomal degradation, whereas formation through Lysine63 linkages is involved in the DNA damage/repair pathway. A breakthrough in ubiquitin research that allowed scientists to reveal and understand the multiple functions of ubiquitin was the chemical synthesis of distinct ubiquitin chains. Chemical synthesis provides the unique advantage that ubiquitin chains can be produced of defined topology (amino acid linkage) and length. Additionally, many of chemically synthesised reagents can be rapidly and efficiently tailored to specific requirements. The development and application of chemical synthesis of ubiquitin polymers has revolutionised the field and created a significant economic market for start-up companies. Ubiquitin belongs to a family of related proteins called ubiquitin-like molecules (Ubls), including Nedd8 and SUMO. These proteins are similar to ubiquitin but distinct conjugation pathways and regulated process exist for each molecule. The ubiquitin-like molecule Nedd8 is essential for viability, growth and development. Components of the Nedd8 pathway are found deregulated in many cancers and inhibitors of Neddylation are in Phase II clinical trials for the treatment of cancer. Compared to 8 available amino acids through which ubiquitin can form polymers, Nedd8 has 10 conserved residues. However, in contrast to ubiquitin, our knowledge on Nedd8 polymerisation is limited. Our recent proteomic and biological studies revealed the formation of Nedd8 chains through most if not all possible linkages. In particular we identified and characterised two distinct classes of Nedd8 chains: the formation through distinct lysines of poly-Nedd8 and hybrid Nedd8-ubiquitin chains. Importantly, we have now assigned their biological functions. We found that poly-Nedd8 chains inhibit the DNA damage-induced apoptosis, whereas hybrid Nedd8-ubiquitin chains are involved in the cellular response to proteotoxic stress. Therefore, Nedd8 has the ability to create diverse cellular signals with distinct biological outcomes. We are now in a unique position to exploit and understand the biological significance of the “Nedd8 code”. For example a key, but still poorly understood issue is the recognition and “decoding” of Nedd8 chains. To achieve this goal the chemical synthesis of distinct Nedd8 chains of defined length and topology will be essential. The purpose of the proposal is to develop a series of chemically synthesized Nedd8 chains (poly-Nedd8 vs hybrid Nedd8/ubiquitin chains. These chains will be used to: 1. Test how de-conjugating enzymes recognise different types of Nedd8 chains. 2. How Nedd8 chains are degraded by the proteasome degradation machinery. 3. To use these chains as a chemical biology tool to identify binding partners in extracts either from tissue culture human cells or from C. elegans, a model organism system used in our laboratory. We expect that these experiments will help us to understand how Nedd8 controls the response to genotoxic and proteotoxic stress.