The document discusses the discovery of Lokiarchaeota, a new archaeal lineage related to the TACK superphylum. Phylogenomic analyses place Lokiarchaeota as the nearest relative of eukaryotes. Interestingly, the genome of Lokiarchaeota encodes many eukaryotic-specific features, such as distant homologs of actin and tubulin, ESCRT complex proteins involved in cell division, and proteins related to transcription and translation. This provides unique insights into the emergence of cellular complexity in eukaryotes and suggests the archaeal ancestor was more complex than previously known archaeal lineages. The genome content of Lokiarchaeota holds clues about the nature of the archaeal ancestor

1. Class 3:
MIB200
Biology of Organisms without Nuclei
Class #3:
A New View of the Tree of Life
UC Davis, Fall 2019
Instructor: Jonathan Eisen
1

4. Class 4:
MIB200
Biology of Organisms without Nuclei
Class #4
Asgard Archaea
UC Davis, Fall 2019
Instructor: Jonathan Eisen
4

5. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2019
Lokiarchaea named after Loki’s Castle Vent Site

6. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2019
Thorarchaeota
http://sites.utexas.edu/baker-lab/2016/01/29/introducing-thorarchaeota/

7. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2019
Asgard Archaea
Something is Wrong Here

8. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2019
Complaining on Twitter …

9. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2019
Response ..

10. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2019
Helarchaeota

11. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2019
Freya not next ..

12. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2019
Helarchaeota

14. Introduction

15. Cellular life is currently classified into three domains: Bacteria, Archaea and
Eukarya. Whereas the cytological properties of Bacteria and Archaea are
relatively simple, eukaryotes are characterized by a high degree of cellular
complexity, which is hard to reconcile given that most hypotheses assume a
prokaryote-to-eukaryote transition1,2. In this context, it seems particularly
difficult to account for the suggested presence of the endomembrane system, the
nuclear pores, the spliceosome, the ubiquitin protein degradation system, the
RNAi machinery, the cytoskeletal motors and the phagocytotic machinery in the
last eukaryotic common ancestor (ref. 3 and references therein). Ever since the
recognition of the archaeal domain of life by Carl Woese and co-workers4,5,
Archaea have featured prominently in hypotheses for the origin of eukaryotes,
as eukaryotes and Archaea represented sister lineages in Woese’s ‘universal
tree’5. The evolutionary link between Archaea and eukaryotes was further
reinforced through stud- ies of the transcription machinery6 and the first
archaeal genomes7, revealing that many genes, including the core of the genetic
information-processing machineries of Archaea, were more similar to those of
eukaryotes8 rather than to Bacteria.
Introduction

16. Cellular life is currently classified into three domains: Bacteria, Archaea and
Eukarya. Whereas the cytological properties of Bacteria and Archaea are
relatively simple, eukaryotes are characterized by a high degree of cellular
complexity, which is hard to reconcile given that most hypotheses assume a
prokaryote-to-eukaryote transition1,2. In this context, it seems particularly
difficult to account for the suggested presence of the endomembrane system, the
nuclear pores, the spliceosome, the ubiquitin protein degradation system, the
RNAi machinery, the cytoskeletal motors and the phagocytotic machinery in the
last eukaryotic common ancestor (ref. 3 and references therein). Ever since the
recognition of the archaeal domain of life by Carl Woese and co-workers4,5,
Archaea have featured prominently in hypotheses for the origin of eukaryotes,
as eukaryotes and Archaea represented sister lineages in Woese’s ‘universal
tree’5. The evolutionary link between Archaea and eukaryotes was further
reinforced through stud- ies of the transcription machinery6 and the first
archaeal genomes7, revealing that many genes, including the core of the genetic
information-processing machineries of Archaea, were more similar to those of
eukaryotes8 rather than to Bacteria.
Introduction

17. During the early stages of the genomic era, it also became apparent that
eukaryotic genomes were chimaeric by nature8,9, comprising genes of
both archaeal and bacterial origin, in addition to genes specific to
eukaryotes. Yet, whereas many of the bacterial genes could be traced
back to the alphaproteobacterial progenitor of mitochondria, the nature of
the lineage from which the eukaryotic host evolved remained
obscure1,10–13. This lineage might either descend from a common
ancestor shared with Archaea (follow- ing Woese’s classical three-
domains-of-life tree5), or have emerged from within the archaeal domain
(so-called archaeal host or eocyte-like scenarios1,14–17). Recent
phylogenetic analyses of universal protein data sets have provided
increasing support for models in which eukaryotes emerge as sister to or
from within the archaeal ‘TACK’ superphylum18–22, a clade originally
comprising the archaeal phyla Thaumarchaeota, Aigarchaeota,
Crenarchaeota and Korarchaeota23.
Introduction

18. During the early stages of the genomic era, it also became apparent that
eukaryotic genomes were chimaeric by nature8,9, comprising genes of
both archaeal and bacterial origin, in addition to genes specific to
eukaryotes. Yet, whereas many of the bacterial genes could be traced
back to the alphaproteobacterial progenitor of mitochondria, the nature of
the lineage from which the eukaryotic host evolved remained
obscure1,10–13. This lineage might either descend from a common
ancestor shared with Archaea (follow- ing Woese’s classical three-
domains-of-life tree5), or have emerged from within the archaeal domain
(so-called archaeal host or eocyte-like scenarios1,14–17). Recent
phylogenetic analyses of universal protein data sets have provided
increasing support for models in which eukaryotes emerge as sister to or
from within the archaeal ‘TACK’ superphylum18–22, a clade originally
comprising the archaeal phyla Thaumarchaeota, Aigarchaeota,
Crenarchaeota and Korarchaeota23.
Introduction

19. In support of this relationship, comparative genomics analyses have revealed
several eukaryotic signature proteins (ESPs)24 in TACK lineages, including
distant archaeal homologues of actin25 and tubulin26, archaeal cell division
proteins related to the eukaryotic endosomal sorting complexes required for
transport (ESCRT)-III complex27, and several information-processing
proteins involved in transcription and translation2,17,23. These findings
suggest an archaeal ancestor of eukaryotes that might have been more
complex than the archaeal lineages identified thus far2,23,28. Yet, the
absence of missing links in the prokaryote-to-eukaryote transition currently
precludes detailed predictions about the nature and timing of events that
have driven the process of eukaryogenesis1,2,17,28. Here we describe the
discovery of a new archaeal lineage related to the TACK superphylum that
represents the nearest relative of eukaryotes in phylogenomic analyses, and
intriguingly, its genome encodes many eukaryote-specific features,
providing a unique insight in the emergence of cellular complexity in
eukaryotes.
Introduction

20. In support of this relationship, comparative genomics analyses have revealed
several eukaryotic signature proteins (ESPs)24 in TACK lineages, including
distant archaeal homologues of actin25 and tubulin26, archaeal cell division
proteins related to the eukaryotic endosomal sorting complexes required for
transport (ESCRT)-III complex27, and several information-processing
proteins involved in transcription and translation2,17,23. These findings
suggest an archaeal ancestor of eukaryotes that might have been more
complex than the archaeal lineages identified thus far2,23,28. Yet, the
absence of missing links in the prokaryote-to-eukaryote transition currently
precludes detailed predictions about the nature and timing of events that
have driven the process of eukaryogenesis1,2,17,28. Here we describe the
discovery of a new archaeal lineage related to the TACK superphylum that
represents the nearest relative of eukaryotes in phylogenomic analyses, and
intriguingly, its genome encodes many eukaryote-specific features,
providing a unique insight in the emergence of cellular complexity in
eukaryotes.
Introduction

21. Don’t Forget Supplemental Information

23. Figure 2 | Metagenomic reconstruction and phylogenetic
analysis of Lokiarchaeum. a, Schematic overview of the
metagenomics approach. BI, Bayesian inference; ML,
maximum likelihood. b, Bayesian phylogeny of
concatenated alignments comprising 36 conserved
phylogenetic marker proteins using sophisticated models of
protein evolution (Methods), showing eukaryotes branching
within Lokiarchaeota. Numbers above and below branches
refer to Bayesian posterior probability and maximum-
likelihood bootstrap support values, respectively. Posterior
probability values above 0.7 and bootstrap support values
above 70 are shown. Scale indicates the number of
substitutions per site. c, Phylogenetic breakdown of the
Lokiarchaeum proteome, in comparison with proteomes of
Korarchaeota, Aigarchaeota (Caldiarchaeum) and
Miscellaneous Crenarchaeota Group (MCG) archaea.
Category ‘Other’ contains proteins assigned to the root of
cellular organisms, to viruses and to unclassified proteins

28. Actins

30. In eukaryotes, the ESCRT machinery represents an essential com-
ponent of the multivesicular endosome pathway for lysosomal
degradation of damaged or superfluous proteins, and it plays a role in
several budding processes including cytokinesis, autophagy and viral
budding44. The ESCRT machinery generally consists of the ESCRT-
I–III subcomplexes, as well as associated subunits45. The analysis of
the Lokiarchaeum genome revealed the presence of an ESCRT gene
cluster (Fig. 4a), as well as of several additional pro- teins
homologous to components of the eukaryotic multivesicular
endosome pathway.

32. We have identified and characterized the genome of Lokiarchaeota, a novel, deeply
rooting clade of the archaeal TACK superphylum, which in phylogenomic analyses of
universal proteins forms a mono- phyletic group with eukaryotes. While the obtained
phylogenomic resolution testifies to a deep archaeal ancestry of eukaryotes, the
Lokiarchaeum genome content holds valuable clues about the nature of the archaeal
ancestor of eukaryotes, and about the process of eukaryogenesis. Many of the ESPs
previously identified in different TACK lineages are united in Lokiarchaeum, indicating
that the patchy distribution of ESPs amongst archaea is most likely the result of lineage-
specific losses2 (Fig. 5). Moreover, the Lokiarchaeum genome significantly expands the
total number of ESPs in Archaea, lending support to the observed phylogenetic
affiliation of Lokiarchaeota and eukaryotes. Finally, and importantly, sequence-based
functional pre- dictions for these new ESPs indicate a predominance of proteins that
play pivotal roles in various membrane remodelling and vesicular trafficking processes
in eukaryotes. It is also noteworthy that Lokiarchaeum appears to encode the most
‘eukaryotic-like’ ribosome identified in Archaea thus far (Supplementary Discussion 4),
including a putative homologue of eukaryotic ribosomal protein L22e (Fig. 5;
Supplementary Fig. 24 and Supplementary Tables 7 and 8).

33. Taken together, our data indicate that the archaeal ancestor of eukar- yotes was even more
complex than previously inferred2 and allow us to speculate on the timing and order of several
key events in the process of eukaryogenesis. For example, the identification of archaeal genes
involved in membrane remodelling and vesicular trafficking processes indicates that the
emergence of cellular complexity was already under- way before the acquisition of the
mitochondrial endosymbiont, which now appears to be a universal feature of all
eukaryotes28,37,50. Indeed, based upon our results it seems plausible that the archaeal ancestor
of eukaryotes had a dynamic actin cytoskeleton and potentially endo- and/or phagocytic
capabilities, which would have facilitated the invagination of the mitochondrial progenitor.
The present identification and genomic characterization of a novel archaeal group that shares a
common ancestry with eukaryotes indi- cates that the gap between prokaryotes and eukaryotes
might, to some extent, be a result of poor sampling of the existing archaeal diversity.
Environmental surveys have revealed the existence of a plethora of uncultured archaeal lineages,
and some of these likely represent even closer relatives of eukaryotes. Excitingly, the genomic
exploration of these archaeal lineages has now come within reach. Such endeavours, combined
with prospective studies focusing on uncovering metabolic, chemical and cell biological
properties of these lineages, will uncover further details about the identity and nature of the
archaeal ancestor of eukaryotes, shedding new light on the evolutionary dark ages of the
eukaryotic cell.