E3-Ubiquitin Ligases as a Use-Case Scenario For Developing Quaternary Protein Complex Ontologies

For the most part, proteins contribute to biological function as subunit components of higher-order quaternary complexes involving other proteins in various states of post-translational modification, assembly and compartmentation. Interest is rapidly growing for the development of an ontology framework to represent the current knowledge in this area, beginning with the assignment of entities and relationships involving protein assemblies of modest complexity as objects with defined subunit content. We have proposed the use of plant E3 Ubiquitin ligase complexes as a use-case scenario for modeling higher-order protein quaternary complex ontologies - in part due to the combinatorial diversity of such complexes in plants. Elements of an ontology framework are therefore proposed that incorporate higher-order protein complex formation based upon E3-Ubiquitin ligases as a model. In many organisms, the existence of specific complexes is known to be regulated via differential subunit expression across developmental time and space, coupled with specific protein abundance and interaction affinity profiles. In some cases, E3 complex formation and/or compartmentation is dependent upon environmental factors, thus offering opportunities for integrating elements of Environment Ontology (EO) into a useful framework where knowledge relating to the conditional formation of plant E3 ligase complexes can be appropriately represented.