G protein-coupled receptors (GPCRs) comprise a superfamily of membrane proteins whose associated signalling pathways control crucial physiological functions. Although this superfamily originated from duplication events, the duplication history of the receptors and their pathway interactors is largely unknown. By using a system-level approach, this work aimed at characterising the duplication patterns among the GPCR signalling system components and establishing their role in disease development and accumulation of genetic variation across the pathway. A comprehensive data set including upstream, downstream and peripheral regulatory and crosstalk components was used to determine the frequency of gene duplication within the GPCR signalling system components. We find that the duplication retention frequency was not constant and that the signalling components tend to differ in their peak frequencies of duplication over evolutionary time, with the exception of whole-genome duplication (WGD). Analysis of GPCR subsets with selective ligand binding and G protein coupling profiles revealed that specific interaction types relate to duplication frequency and tissue specificity. We also find that the evolutionary origin of gene expression in most tissues was influenced by the duplication history of the signalling components, highlighting the importance of duplication and divergence in the evolution of GPCR signalling in specific tissues and cell types. Disease-associated genes within the GPCR signalling system were further analysed with regard to their duplication history. We found that most disease associated genes are WGDs (ohnologues) in all signalling components, although duplicate genes are not overrepresented within ligands. Disease incidence is associated with the most ancient signalling components (G proteins and downstream signalling effectors) and tends to be inherited in an autosomal dominant manner, suggesting that genes within these components are dosage-balanced. We also found that the highest percentages of complex diseases are associated within ligands and GPCRs, indicating that the duplication events that expanded the pathway also created more opportunities for disease to emerge. Heritable genetic variation was also investigated within the GPCR signalling system. We found that the majority of pathway genes tend to accumulate more variation than protein-coding genes, and that for GPCRs this is not due to more transcript isoforms resulting from alternative splicing. A relationship between the accumulation of genetic variation and duplication patterns could not be established, however, differences within variant predicted effects point to distinct selective pressures across the pathway. Highly disruptive mutations indicate that upstream ligands are the least constrained elements, and an excess of intronic variants suggests that downstream signalling effectors are more evolutionarily constrained. The findings in this thesis expand the knowledge of this signalling system and contribute to a better understanding of the evolution of disease and interpretation of genetic variation in a system-wide context.
|Date of Award||1 Aug 2019|
- The University of Manchester
|Supervisor||David Robertson (Supervisor) & Jean-Marc Schwartz (Supervisor)|
- gene and genome duplication
- signalling pathway