The TRIM (TRipartite Motif) Family as a Novel Class of Ubiquitin E3 Ligases

Napolitano, Luisa Maria Rosaria (2011). The TRIM (TRipartite Motif) Family as a Novel Class of Ubiquitin E3 Ligases. PhD thesis The Open University.

DOI: https://doi.org/10.21954/ou.ro.0000f1a9

Abstract

Proteins that belong to TRIM family are characterized by the presence of the tripartite motif module, composed of a RING domain, one or two B-box domains and a Coiled-coil region. TRIM proteins are involved in several cellular processes such as apoptosis, cell cycle regulation and viral response. The aim of my project was to study the involvement of TRIM proteins in the ubiquitylation process, a versatile post-translational modification mechanism used by eukaryotic cells mainly to control proteins levels through proteasome-mediated proteolysis. In particular, the presence of the RING domain and experimental data suggested a possible TRIM role as Ubiquitin Ligases (E3), the component of the ubiquitylation cascade responsible for the transfer of Ubiquitin to the specific target.

A condition for being an E3 is the interaction with another component of the ubiquitylation cascade, the Ubiquitin Conjugating Enzymes (UBE2). Therefore, I tested the interaction between 26 UBE2 enzymes and 42 TRIM proteins. I observed that the majority of the TRIM proteins tested interact with UBE2 enzymes and I also found a general preference of the TRIM proteins for the D and E classes. Two important exceptions were observed: TRIM9-UBE2G2 and TRIM32-UBE2V1/2 specific interactions. Furthermore, representative interactions were confirmed and I also demonstrated that the TRIM E3 activity is only manifest with the UBE2 they interact with. For most specific interactions I could also observe subcellular co-localisation of the TRIM involved and its cognate UBE2 enzyme suggesting that the specific selection of TRIM-UBE2 pairs has physiological relevance.

In addition I found that almost all TRIM proteins tested interacted with UBE2I that is the specific E2 enzyme involved in modification with SUMO, a Ubiquitin-like peptide. Consistently, representative interactions were confirmed and for a subset of TRIM proteins I demonstrated the involvement in the SUMOylation pathway suggesting a possible cross-talk between ubiquitylation and SUMOylation.