Tracing the Archaeal Origins of Eukaryotic Membrane-Trafficking System Building Blocks

Abstract

In contrast to prokaryotes, eukaryotic cells are characterized by a complex set of internal membrane-bound compartments. A subset of these, and the protein machineries that move material between them, define the membrane-trafficking system (MTS), the emergence of which represents a landmark in eukaryotic evolution. Unlike mitochondria and plastids, MTS organelles have autogenous origins. Much of the MTS machinery is composed of building blocks, including small GTPase, coiled-coil, beta-propeller + alpha-solenoid, and longin domains. Despite the identification of prokaryotic proteins containing these domains, only few represent direct orthologues, leaving the origins and early evolution of the MTS poorly understood. Here, we present an in-depth analysis of MTS building block homologues in the composite genome of Lokiarchaeum, the recently discovered archaeal sister clade of eukaryotes, yielding several key insights. We identify two previously unreported Eukaryotic Signature Proteins; orthologues of the Gtr/Rag family GTPases, involved in target of rapamycin complex signaling, and of the RLC7 dynein component. We could not identify golgin or SNARE (coiled-coil) or beta-propeller + alpha-solenoid orthologues, nor typical MTS domain fusions, suggesting that these either were lost from Lokiarchaeum or emerged later in eukaryotic evolution. Furthermore, our phylogenetic analyses of lokiarchaeal GTPases support a split into Ras-like and Arf-like superfamilies, with different prokaryotic antecedents, before the advent of eukaryotes. While no GTPase activating proteins or exchange factors were identified, we show that Lokiarchaeum encodes numerous roadblock domain proteins and putative longin domain proteins, confirming the latter's origin from Archaea. Altogether, our study provides new insights into the emergence and early evolution of the eukaryotic membrane-trafficking system.

The changing view of eukaryogenesis – fossils, cells, lineages and how they all come together

“…Using metagenomics, Spang et al have recently obtained the first genomic data from uncultured members of the deep-sea archaeal group (DSAG) lineage, which is related to the TACK superphylum, and proposed a new phylum called 'Candidatus Lokiarchaeota' (Spang et al, 2015). Their data suggest that Lokiarchaeota are the archaeal lineage closest to Eukaryota, and revealed the presence of a large set of eukaryotic signature proteins that previously had only been seen in diverse TACK members, and, once more, the presence of proteins related to the eukaryotic cytoskeleton components (Klinger et al, 2016;Spang et al, 2015).…”

“…The Lokiarchaeota phylum yields tantalizing insights as it features extensive complements of GTPases and the first reported presence of longin domains in a non-eukaryotic genome (Klinger et al, 2016). Longin domains are present in conserved eukaryotic protein superfamilies and had previously been believed to be exclusive to eukaryotes.…”

“…Longin domains are present in conserved eukaryotic protein superfamilies and had previously been believed to be exclusive to eukaryotes. However, despite the presence of these proteins in Archaea, there are no direct orthologues of the Rab and ARF GTPase sub-families that have specific cellular functions in eukaryotes (Klinger et al, 2016). The Lokiarchaeota composite genome also contains the most extensive group of archaeal homologues of the ESCRT machinery yet described, which has a conserved role in cytokinesis, in both archaeal and eukaryotic cells (Makarova et al, 2010), as well as functions in late endosomal trafficking in eukaryotes.…”

“…Tubulin-like proteins are present in the Verrucomicrobia (Pilhofer et al, 2007). There are many distinct actin-like families in archaea, for example Crenactin, restricted to the Korarchaeota, Aigarchaeota, Lokiarchaeota and some Crenarchaeota (Spang et al, 2015), and there are some cytoskeletal protein orthologues specific to Lokiarcheota (Klinger et al, 2016;Spang et al, 2015). Demonstration of the TACK archaea as the lineages potentially closest to the one that gave rise to the Eukarya has profound implications for how we view such evidence.…”

“…In addition, there is a third group of genes that represents strictly eukaryotic innovations and, thus, includes a substantial proportion of the genes required to build and define many intracellular compartments. Although some of these features are likely of prokaryotic ancestry, there is a considerable expansion of the associated gene families, and their elaboration makes them true eukaryotic innovations (Klinger et al, 2016).…”