Lowest Universal Common Ancestor - LUCA
Probably the ancestor of the bacteria and archaea – so a prokaryote!
The traits of LUCA are the ones most basal – shared by virtually all living organisms
- Based on parsimony – shared traits are inherited from a common ancestor but
fundamentally distinct traits arose independently in each group
So LUCA presumably had:
RNA, DNA, transcription, translation, ribosomes, rotor-stator type ATPase, ATP,
Krebs cycle (partly – acetyl coA pathway - seen in primitive methanogens, acetogens,
congruence with chemistry in vents?)
- ATPase can also be an ancestral component present in LUCA – Archaea and
bacteria possess similar ATP synthase enzymes
Some argue that ATP synthase is too structurally complex to have evolved so
early
Though there are many other methods of tapping an external proton gradient to
cell physiology eg. Pyrophosphate can be formed from phosphate and H+
gradient
Can overcome by chemiosmosis (LUCA is chemiosmotic, regardless!), though
delocalised proton gradient
Similarly, fermentation could’ve evolved twice – LUCA unable to perform
fermentations
Fermentation evolved later, after autotrophs produced organic compounds (reasons
suggested in previous lecture) – LUCA was more likely chemisosmotic
3 domain hypothesis vs. Eocyte hypothesis
Genomic evidence suggests that the eukaryotic
cell arose via a stochastic endosymbiosis
between 2 prokaryotes
- Moderately strong phylogenomic evidence
suggests LUCA was a prokaryote
Eocyte hypothesis first proposed in 1984
by Lake et al., to challenge Woese’s 3
domains of life
- Based on analysis on ribosome structure
– eukaryotes share close ancestry with
some lineages of archaea and not others
– archaeal ancestors of eukaryotes eocytes
- Embley et al., - 41 proteins in 35 species: eocyte tree supported
- Phylogenomic studies show that eukaryotes branch within archaea – hence only 2
primary domains (eukaryotic host cell was an archaeon) (Williams et al., 2013)
Eukaryotes have mosaic genomes – though 75% of all eukaryote genes are more
, closely related to genes found in bacteria than ones in archaea (possibly obtained by
HGT)
- Archaeal gene tend to be involved in information processing
- Bacterial genes tend to be associated with metabolism and structure of the cell
- Koonin et al., found proteins that make up walls of the nucleus are made up of
both archaeal and bacterial genes
Full genome studies root tree of life between archaea and bacteria – implies LUCA
was thermophilic, chemiosmotic, autotrophic – Stetter, 2006, Dagan et al., 2010
The paradox of LUCA’s traits
Although bacteria and archaea share some fundamental biochemical traits, there
are many elements they do not share: cell membrane, enzymes for lipid synthesis,
cell wall, glycolysis, DNA replication, respiratory chains
Cell membrane lipids
Archaeal phospholipids: isoprene
side-chains joined by an ether bond
to L-glycerol
Bacterial phospholipids: long-chain
fatty acids joined by ester bonds to
D-glycerol
Enzymes required are distinct in the 2 domains
LUCA had RNA, DNA and the genetic code but could not replicate DNA – a
retroviral lifecycle (in vent pores – unlikely, reverse transcriptase is not ubiquitous)
LUCA was chemiosmotic and could tap proton gradients, but did not have a modern
phospholipid membrane
Implication: bacteria and archaea emerged independently from a common ancestor
in alkaline vents – credible explanation?
Differences in cell wall
Bacteria: murein (peptidoglycan) – N-acetylmuranmic acid + N-acetyl-o-glucosamine
(NAG) linked by β(1,4) glycosidic bonds
Archaea: pseudomurein – N-acetyltalosaminuronic (NAT) and NAG connected
through β(1,3) glycosidic linkages
Murein and pseudomurein cell walls similar in structure and function, but
fundamentally different in biosynthetic pathways and chemistry – suggests
convergent evolution
Alternative explanations
1. Bacterial lipids ancestral, archaeal lipids replaced them during adaptation to
hyperthermophilic environments (but many bacteria are hyperthermophilic, and
Probably the ancestor of the bacteria and archaea – so a prokaryote!
The traits of LUCA are the ones most basal – shared by virtually all living organisms
- Based on parsimony – shared traits are inherited from a common ancestor but
fundamentally distinct traits arose independently in each group
So LUCA presumably had:
RNA, DNA, transcription, translation, ribosomes, rotor-stator type ATPase, ATP,
Krebs cycle (partly – acetyl coA pathway - seen in primitive methanogens, acetogens,
congruence with chemistry in vents?)
- ATPase can also be an ancestral component present in LUCA – Archaea and
bacteria possess similar ATP synthase enzymes
Some argue that ATP synthase is too structurally complex to have evolved so
early
Though there are many other methods of tapping an external proton gradient to
cell physiology eg. Pyrophosphate can be formed from phosphate and H+
gradient
Can overcome by chemiosmosis (LUCA is chemiosmotic, regardless!), though
delocalised proton gradient
Similarly, fermentation could’ve evolved twice – LUCA unable to perform
fermentations
Fermentation evolved later, after autotrophs produced organic compounds (reasons
suggested in previous lecture) – LUCA was more likely chemisosmotic
3 domain hypothesis vs. Eocyte hypothesis
Genomic evidence suggests that the eukaryotic
cell arose via a stochastic endosymbiosis
between 2 prokaryotes
- Moderately strong phylogenomic evidence
suggests LUCA was a prokaryote
Eocyte hypothesis first proposed in 1984
by Lake et al., to challenge Woese’s 3
domains of life
- Based on analysis on ribosome structure
– eukaryotes share close ancestry with
some lineages of archaea and not others
– archaeal ancestors of eukaryotes eocytes
- Embley et al., - 41 proteins in 35 species: eocyte tree supported
- Phylogenomic studies show that eukaryotes branch within archaea – hence only 2
primary domains (eukaryotic host cell was an archaeon) (Williams et al., 2013)
Eukaryotes have mosaic genomes – though 75% of all eukaryote genes are more
, closely related to genes found in bacteria than ones in archaea (possibly obtained by
HGT)
- Archaeal gene tend to be involved in information processing
- Bacterial genes tend to be associated with metabolism and structure of the cell
- Koonin et al., found proteins that make up walls of the nucleus are made up of
both archaeal and bacterial genes
Full genome studies root tree of life between archaea and bacteria – implies LUCA
was thermophilic, chemiosmotic, autotrophic – Stetter, 2006, Dagan et al., 2010
The paradox of LUCA’s traits
Although bacteria and archaea share some fundamental biochemical traits, there
are many elements they do not share: cell membrane, enzymes for lipid synthesis,
cell wall, glycolysis, DNA replication, respiratory chains
Cell membrane lipids
Archaeal phospholipids: isoprene
side-chains joined by an ether bond
to L-glycerol
Bacterial phospholipids: long-chain
fatty acids joined by ester bonds to
D-glycerol
Enzymes required are distinct in the 2 domains
LUCA had RNA, DNA and the genetic code but could not replicate DNA – a
retroviral lifecycle (in vent pores – unlikely, reverse transcriptase is not ubiquitous)
LUCA was chemiosmotic and could tap proton gradients, but did not have a modern
phospholipid membrane
Implication: bacteria and archaea emerged independently from a common ancestor
in alkaline vents – credible explanation?
Differences in cell wall
Bacteria: murein (peptidoglycan) – N-acetylmuranmic acid + N-acetyl-o-glucosamine
(NAG) linked by β(1,4) glycosidic bonds
Archaea: pseudomurein – N-acetyltalosaminuronic (NAT) and NAG connected
through β(1,3) glycosidic linkages
Murein and pseudomurein cell walls similar in structure and function, but
fundamentally different in biosynthetic pathways and chemistry – suggests
convergent evolution
Alternative explanations
1. Bacterial lipids ancestral, archaeal lipids replaced them during adaptation to
hyperthermophilic environments (but many bacteria are hyperthermophilic, and
