Transcript The Practical Guide to Prokaryotic Metabolisms: Ancient

The Last Common
Ancestor and the
Three Domains of
Life or….
A Case History of the only current
example of life that we have..
• Trees, domains, and ancestry..
• Where does the whole idea come from?
16S rRNA
Chop into pieces with enzymes
Separate pieces with 2D electrophoresis gel
Creates fingerprint
Sequence and catalogue each spot
Phylogenetic structure of the prokaryotic domain: the primary
kingdoms, PNAS November 1, 1977 vol. 74 no. 11 5088-5090
These observations gave rise to…
• The root of the tree
• The idea of a last common ancestor
• The role of horizontal gene transfer vs
lateral transfer
Tree Structure
• Bifurcating – sex vs clonal
• Rooting
Time
Now
Then
Gogarten et al and Miyata et al in 1989, used ancient duplication event
to root the tree that separated the bacteria from the archaea/eukaryotes
Mosaic nature of genomes once
we started sequencing them.
We can now sequence a
genome in a week… if you have
the money… even that’s getting
cheaper..
Complex -> Simple, Forterre
et al
All attempts to reconcile
various nucleic acid
datasets
Ring of Life,
Lakes et al
Last Common Ancestor
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LUCA – last universal common ancestor
LUA – last universal ancestor
Cenancestor (number one)
MRCA – most reacent common ancestor
Properties shared by all living
organisms
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Genetic code based on 4 nucleotides
3 letter codons, 20 AA,
DNA repair
DNA polymerase, double stranded DNA maintained
single stranded RNA intermediate
genetic code expressed in proteins
Ribosomes
ATP as energy currency
lipid bilayers as cellular membrane
intracellular sodium is lower, phosphorus is higher and
mainatined by ion pumps
COMPLEX
• cell division
LUCA
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Not a simple, primitive, hyperthermophilic prokaryote
a complex community of protoeukaryotes with a RNA genome, adapted to a broad range of
moderate temperatures, genetically redundant, morphologically and metabolically diverse.
LUCA's genetic redundancy predicts loss of paralogous gene copies in divergent lineages to
be a significant source of phylogenetic anomalies, i.e. instances where a protein tree departs from
the SSU-rRNA genealogy
horizontal gene transfer may not have the rampant character assumed by many.
Examining membrane lipids suggest LUCA had sn1,2 ester fatty acid lipids from which Archaea
emerged from the outset as thermophilic by "thermoreduction," with a new type of membrane,
composed of sn2,3 ether isoprenoid lipids; this occurred without major enzymatic reconversion.
Bacteria emerged by reductive evolution from LUCA and some lineages further acquired
extreme thermophily by convergent evolution.
This scenario is compatible with the hypothesis that the RNA to DNA transition resulted from
different viral invasions as proposed by Forterre.
Beyond the controversy opposing "replication first" to metabolism first", the predictive arguments
of theories on "catalytic closure" or "compositional heredity" heavily weigh in favour of LUCA's
ancestors having emerged as complex, self-replicating entities from which a genetic code arose
under natural selection.
Glansdorff, Xu, & Labedan, 2008, Biology Direct
Ancestor was hypothesized, based on
gene trees and the genetic distance
between living cells and fossils to be 3.5
to 3.9 GA
Possible caveats
• Some lineages went extinct
• genetic heritage of all modern organisms
derived through horizontal gene transfer
among an ancient community of
organisms.
• panspermia.
• Confounding the picture of the three
domains of life and the concept of the last
common ancestor, is the reality of
Horizontal Gene Transfer
Quick facts
• When you do phylogenetic reconstruction
on rRNA’s, in >15,000 sequences, about
99% of the time, DO NOT appear to
horizontally transfer.
• Margaret Dayhoff, physical chemist, and
the mother of bioinformatics, based all her
metrics on the assumption that genes did
not move horizontally.
How do you find HGT
• Sequence context
(recent events)
– G+C content,
codon usage
• Phylogenetic
incongruencies
(more ancient
events)
Doolittle, SciAmer
An alternative if to choose
metabolic pathways that might
have been integral to HGT events
and the evolution of life
Ability to fix nitrogen found in wide variety of
prokaryotes (bacteria and archaea)
Singular origin of nif genes though they show a
paraphyletic distribution - horizontal gene
transfer (HGT), selective loss?
Nif gene homologs have been recruited
from/into many pathways, including
bacteriochlorophyll biosynthesis, FeS cluster
assembly and insertion, hydrogenase,
regulation of heterocyst differentiation
Nif genes sometimes found on plasmids (in
rhizobia); facilitation of HGT?
Alternative nitrogenases
Nif D, K
NifH
nifH
nifD
niK
nifE
nifN
Raymond et
al, 2004
Interdisciplinary approaches…
• To understand the genetic record of earth
life and the LCA, we have to understand
the ecology in which life evolved… from
the individual micro environments that may
have been present to the elemental
abundances provided by the unique place
we occupy in space.
• Another sample would be nice… really
nice.
If we know what to do with it…
Janet, did you ever wonder why
as we get older we become more
careful and less willing to take a
chance, when we really have
nothing to lose. And young
people, they have everything
ahead of them, and yet take so
many chances… you would have
thought evolution would have
wired our brains differently than
that…
12 January 1927 – 27
October 2007)
Never underestimate the complex, improbable beauty and creative
potential of evolution. The conundrums keep us guessing.