Reconciling Asgardarchaeota Phylogenetic Proximity to Eukaryotes and Planctomycetes Cellular Features in the Evolution of Life

Abstract

The relationship between the three domains of life—Archaea, Bacteria and Eukarya—is one of Biology’s greatest mysteries. Current favored models imply two ancestral domains, Bacteria and Archaea, with eukaryotes originating within Archaea. This type of models has been supported by the recent description of the Asgardarchaeota, the closest prokaryotic relatives of eukaryotes. However, there are many problems associated with any scenarios implying that eukaryotes originated from within the Archaea, including genome mosaicism, phylogenies, the cellular organization of the Archaea, and their ancestral character. By contrast, all models of eukaryogenesis fail to consider two relevant discoveries: the detection of membrane coat proteins, and of phagocytosis-related processes in Planctomycetes, which are among the bacteria with the most developed endomembrane system. Consideration of these often overlooked features and others found in Planctomycetes and related bacteria suggests an evolutionary model based on a single ancestral domain. In this model the proximity of Asgard and eukaryotes is not rejected but instead, Asgard are considered as diverging away from a common ancestor instead of on the way towards the eukaryotic ancestor. This model based on a single ancestral domain solves most of the ambiguities associated with the ones based on two ancestral domains. The single-domain model is better suited to explain the origin and evolution of all three domains of life, blurring the distinctions between them. Support for this model as well as the opportunities that it presents not only for re-interpreting previous results, but also for planning future experiments, are explored.

Cultured deep-sea PVC bacteria shed light on eukaryogenesis

“…This scenario supports a 2D model of evolution in which bacteria and archaea evolved along two separate branches of the tree of life, and eukaryotes evolved from archaea 37 . Here, at a cell biological and transcriptome level, we discovered more developed eukaryotic features in deep-sea PVC bacteria than previously reported, most notably a nucleolus-containing nucleus and mitosis, supporting the alternative and recent hypothesis of PVC-based eukaryogenesis 10 . Based on our data, we propose a modified PVC-based linear (1D) scenario of eukaryogenesis (Fig.…”

“…Consistently, earlier work proposed that the ancestor of the PVC bacteria diverged by developing distinct features that would later become known as archaeal, eukaryotic, or shared between them 10 . The PVC bacteria are thought to be the sister taxa to the LAECA lineage and the root of the Archaea and eukaryotes 10 . However, the objectivity and accuracy of this scenario need to be further clarified through culturing PVC bacteria that possessing more significant eukaryotic signatures (e.g.…”

“…Lentisphaerae and Kirimatiellaeota as well as some uncultured candidate phyla) are examples of bacteria with features usually associated with eukaryotes or archaea, or both [10][11][12] , and hence represent exceptions to how we define bacteria. Consistently, earlier work proposed that the ancestor of the PVC bacteria diverged by developing distinct features that would later become known as archaeal, eukaryotic, or shared between them 10 . The PVC bacteria are thought to be the sister taxa to the LAECA lineage and the root of the Archaea and eukaryotes 10 .…”

“…Conversely, the endosymbiotic hypotheses propose that a moderately large and anaerobic prokaryote engulfed aerobic bacteria, some of which escaped digestion and instead became stabilized as endosymbionts, eventually evolving into mitochondria 8,9 . Testing these theories has been difficult given the reliance of canonical models unlikely to capture the wider spectrum of prokaryote cell biology and the paucity of known intermediate stages in the prokaryote-to-eukaryote transition 1,10 . However, if eukaryotes evolved from prokaryotes, then there must have been viable organisms with intermediate cellular structures and life styles between prokaryotes and eukaryotes 1,10 , and investigating such intermediates therefore holds the potential to decode the mysterious eukaryogenesis process.…”

Editorial: Structure, Function and Evolution of Complex Cellular Organization in Bacteria and Archaea

“…Perhaps in contrast to the connections being made between Asgard lineages and eukaryote cell complexity, his analysis suggests that Archaea possess a small and relatively homogeneous "vocabulary" in comparison with the greater heterogeneity and complexity observed for Bacteria. Moreover, fold family analysis supports other recent suggestions of an ancient evolutionary link between Bacteria and Eukarya (Devos, 2021), perhaps consistent with some shared basal elements needed for the evolution of compartmentation.…”