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Origin of Eukaryotes: Current Models
Jena Johnson, James Hemp
and Woody Fischer
California Institute of Technology
Unique Modern Eukaryotic Features
•  Nucleus
▫  Double-membrane
•  Endomembrane system
•  Cytoskeleton
▫  Actin and tubulin
▫  Phagocytosis
•  Organelles
▫  Mitochondrion
▫  Chloroplast
•  Spliceosomal introns
•  Linear chromosomes
•  Meiotic sex
▫  Unique cytokinesis
structures
•  Sterol synthesis?
Models for Eukaryote Origin
•  Three domain model
▫  Eukaryotes are distinct forms of life
–  Archaea, Bacteria, Eukaryotes
▫  Ancestrally amitochondrial
•  Two domain models
▫  Nucleated Eukaryotes evolved from Archaea
–  May have involved an early endosymbiosis event
–  Ancestrally amitochondrial
–  Mitochondria were acquired later
▫  Acquisition of the mitochondria in an Archaeon resulted in a
Eukaryote
–  No ancestrally amitochondrial Eukaryotes ever existed
Three Domains vs Two Domains
Gribaldo, 2010
Three Domain Model (Archezoa)
Two Domain Models
Embley & Martin, 2006
Mitochondrial Diversity
Muller, 2012
Diversity of Archaea and Microbial
Eukaryotes
•  The majority of Archaea and
microbial Eukaryotes are
uncultured
•  Genome sequences
▫  < 200 Archaea
▫  < 200 Eukaryotes
▫  > 5000 Bacteria
•  Anaerobes extremely
unrepresented
Eukaryotic evolution, changes and
challenges
T. Martin Embley and William Martin
Figure 1
Figure 2
Figure 3
Figure 4
But, hydrogen sulfide
is toxic and inhibits
respiratory Complex
IV, and why would the
metabolism later switch?
Hydrogen-excreting
bacterium +
methanogenic archaea
... but, this is
incompatible with
oxygen and no evidence
of methanogenic genes
now
Why would the oxygensensitive cell remain on
the outside?
14 2003
Searcy,
Questions
•  Does the current lack of evidence for an ancestrally
amitochondrial Eukaryote condemn the Archezoa
hypothesis?
•  Does a syntrophic origin of Eukaryotes make
ecological sense?
▫  If so, what would have been the original driving force? O2,
H2, H2S, etc.
•  If Archezoa never existed, how did all of the unique
Eukaryote traits evolve?
•  Why would analysis of the same data yield such
diverging hypotheses?
On the evolution of cells
Carl R. Woese
Figure 1
Thoughts and Questions
•  Translation (LCA) ->Transcription (LCA)->
Replication
•  Horizontal gene transfer
▫  Complexity hypothesis
▫  Darwinian threshold
▫  Universal gene pool
–  Hyperparallel vs linear evolution
▫  Why would a universal gene pool still exist in the
presence of Bacteria? Why does it not exist today?
▫  Complexity limit
–  Why are Eukaryotes more complex than Bacteria or Archaea?
•  What evidence would support this model of evolution?
Moving Forward
•  Use metagenomics to understand extant
Eukaryote and Archaea diversity
▫  Look for putative ancestrally amitochondrial
Eukaryotes
–  RNA (16s) and protein encoding genes (RpoB,
RecA,etc.)
•  Sequence more Archaea and Eukaryotes
▫  Single cell sequencing
•  Characterize more α-Proteobacteria near
the mitochondria
▫  What did last common mitochondrial ancestor do?
Environmental RpoB Tree