Ancient Complexity, Opisthokont Plasticity, and Discovery of the 11th Subfamily of Arf GAP Proteins

• Authors: Alexander Schlacht, University of Alberta; Kevin Mowbrey, University of Alberta; Marek Elias, University of Ostrava; Richard A Kahn, Emory University; Joel B. Dacks, University of Alberta
• Journal Title: Traffic
• Volume: Volume 14, Number 6
• Publisher: Wiley: 12 months | 2013-06, Pages 636-649
• Type of Work: Article | Post-print: After Peer Review
• Publisher DOI: http://doi.org/10.1111/tra.12063
• Subjects: Chemistry, Biochemistry; Health Sciences, Human Development; Biology, Neuroscience
• Keywords: membrane traffic; phylogeny; comparative genomics; vesicle transport; GTPase; ADP-ribosylation factors (Arfs); GTPase activating proteins (GAPs); evolutionary cell biology

Abstract

The organelle paralogy hypothesis is one model for the acquisition of non-endosymbiotic organelles, generated from molecular evolutionary analyses of proteins encoding specificity in the membrane traffic system. GTPase Activating Proteins (GAPs) for the ADP-ribosylation factor (Arfs) GTPases are additional regulators of the kinetics and fidelity of membrane traffic. Here we describe molecular evolutionary analyses of Arf GAP protein family. Of the ten subfamilies previously defined in humans, we find that five were likely present in the Last Eukaryotic Common Ancestor (LECA). Of the three more recently derived subfamilies, one was likely present in the ancestor of opisthokonts (animals and fungi) and apusomonads (flagellates classified as the sister lineage to opisthokonts), while two arose in the holozoan lineage. We also propose to have identified a novel ancient subfamily (ArfGAPC2), present in diverse eukaryotes but which is lost frequently, including in the opisthokonts. Surprisingly few ancient domains accompanying the ArfGAP domain were identified, in marked contrast to the extensively decorated human Arf GAPs. Phylogenetic analyses of the subfamilies reveal patterns of single and multiple gene duplications specific to the Holozoa, to some degree mirroring evolution of Arf GAP targets, the Arfs. Conservation, and lack thereof, of various residues in the ArfGAP structure provide contextualization of previously identified functional amino acids and their application to Arf GAP biology in general. Overall, our results yield insights into current Arf GAP biology, reveal complexity in the ancient eukaryotic ancestor, and integrate the Arf GAP family into a proposed mechanism for the evolution of non-endosymbiotic organelles.