Mammalian evolution and human mutation burden in Rab GTPases

Rab GTPases are essential regulators of membrane trafficking with known roles in neurodegeneration, cancer progression and metastasis. While individually, Rabs have been extensively studied in disease and phylogenetic contexts, the overall evolutionary and mutation patterns that influence Rab function, at a family level, remain underexplored. Hence, we performed a family-wide investigation of Rabs in mammalian evolution integrated with disease-related mutations in modern humans. In this study, we analysed 54 Rab proteins across 62 placental mammals using branch-site models, to assess the extent of their sequence evolution across the mammalian lineages. We then combined these findings with the mutation data in human Rabs from UniProt. We defined three domain-level metrics, namely, constraint score, damage tolerance and overall mutation burden, to evaluate how Rab proteins as a whole, and in each of their domains, tolerate variation at the population level in humans. Our results suggest that the Rabs evolving across a larger number of mammalian species tended to show greater accumulation of damaging mutations in humans, particularly within the Switch I domain. This region is critical to Rab function and appears to exhibit cross-species variation while accommodating mutations relevant to human disease. The integrated framework used to examine mammalian Rab evolution and disease-related variation in human Rabs, can also be applied to investigate other conserved protein families implicated in diseases.