Research

Ubiquitination in Eukaryotic Biology

Ubiquitin is a small protein conserved in all eukaryotes. The cell uses ubiquitin to modify many other proteins to modulate their functions. When a protein substrate is modified by a chain of multiple ubiquitin molecules, it will be targeted to the proteasome for degradation. Ubiquitin-dependent protein degradation is involved in the regulation of a large number of important proteins in the cell. Read the review by Dr. Avram Hershko and Dr. Aaron Ciechanover, who won the Nobel Prize in 2004 for their pioneer work on the ubiquitin system.

Ubiquitin has several homologous relatives, including Nedd8, SUMO, and ISG15. These ubiquitin-like proteins are also protein modifiers. Upon covalently attached to a protein in a monomer form, ubiquitin and ubiqutin-like proteins can either present a cellular signal or change the surface property, therefore, biological behavior of the target.

Ubiquitin Ligases

Protein ubiquitination is tightly controlled in eukaryotic cells. This is achieved through the functions of a family of enzymes called ubiquitin ligases. At the end of a three-enzyme (E1-E2-E3) cascade, the ubiquitin E3 ligase catalyzes the transfer of a ubiquitin from the ubiquitin E2 conjugating enzyme to the protein substrate and dictates the specificity of the reaction. A particular ubiquitin ligase usually can only bind one or a limited set of protein substrates. Given the large number of proteins that are controlled by ubiquitin-dependent proteolysis, it is expected that there are hundreds of thousands of ubiquitin ligases in human cells. Read the review by Dr. Cecile Pickart.

Cullin-RING E3 Complexes

The cullin-RING E3 complexes represent the largest family of multi-subunit ubiquitin ligases in eukaryotic cells (for a recent review, see Petroski & Deshaies). Assembled in a modular mode, cullin-RING E3s are built on a catalytic core consisting of a cullin scaffold protein and a RING finger protein. Humans have six closely related cullins, Cul1, 2, 3, 4A, 4B, and 5. Using a unique adaptor, each cullin scaffold can organize a distinct sub-family of E3 complexes by recruiting a group of substrate receptor subunits. Together, these cullin-RING complexes promote the ubiquitination of many well-known regulatory proteins such as the Wnt signaling protein beta-catenin, the NF-kappaB inhibitor IkappaB, the Cyclin-Cdk inhibitor p27, the oxygen-regulated transcription factor HIF1alpha, then antioxidant response transcription factor Nrf2, and the DNA replication licensing factor Cdt1. After having studied the Cul1-based SCF complex, we are now investigating the least understood cullin-RING E3 complex, the DDB1-Cul4A machinery.

All cullin-RING E3s are regulated by a numer of common cellular factors including the ubiquitin-like cullin modifier Nedd8, the cullin inhibitor protein CAND1, and the eight-subunit protein complex, the COP9 signalosome. How such a network of proteins comes together and regulates the functions of cullin-RING E3s is unclear. We are now trying to andress this question via structural biology.

Ubiquitin Ligases and Human Health

As an emerging family of enzymes playing a central role in eukaryotic biology, ubiquitin ligases represent a novel class of potential drug targets. Can we use small molecules to manipulate ubiquitin ligases for therapeutic purpose? For example, can we inhibit the ubiquitination and degradation of a tumor suppressor?

To overcome the defense mechanisms employed by the host, many pathogenic viruses, such as HIV, produce viral proteins that can exploit the cellular ubiquitin ligases to ubiquitinate and eliminate cellular anti-viral factors. Can we develop drugs that can inhibit these viral proteins, thereby, restoring the immune systems that humans have evolved to fight against viral infection?

Our current research is aimed at answering these questions.