Transcript The Origins of Life and Precambrian Evolution

The Origins of Life and
Precambrian Evolution
Chapter 16
1
Questions
• What was the first living thing?
• Where did it come from?
• What was the last common ancestor of
today’s organisms and when did it live?
• What is the shape of the tree of life?
• How did the last common ancestor’s
descendants evolve into today’s organisms?
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Cartoon of the tree of life (Fig. 16.1)
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What is “alive”?
• Living things have:
– the ability to replicate or reproduce, together with the
ability to store and transmit heritable information – to
have a “genotype”
– the ability to express that information – to have a
“phenotype”
– the ability to evolve – to make changes in the heritable
material and to have those changes “tested” in order to
distinguish valuable ones from detrimental ones
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Molecules as living things
• In principle, a molecule could be alive by our
definition:
– If it had the ability to copy itself using raw materials in
its environment, and if errors in copying led to
differences in the speed of self-replication or in
chemical stability
– In this case, the “genotype” is the chemical structure of
the molecule, and the “phenotype” is the speed of selfreplication or stability of the molecule
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Protein vs. nucleic acid
• Proteins possess the enzymatic function that
would presumably be necessary for a selfreplicating molecule – but there is no evidence
that proteins can propagate themselves
• Nucleic acids possess, in principle, the ability to
direct their self-replication via complementary
base-pairing – but until about 20 years ago were
not known to possess any enzymatic function
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The RNA world hypothesis
• Catalytic RNA molecules were a transitional form
between non-living matter and the earliest cells
• In the early 1980’s it was discovered
independently by Sidney Altman and Thomas
Cech that some RNA molecules had enzymatic
activity – specifically, they could form and break
the phosphoester bonds that link adjacent
nucleotides in nucleic acids – ribozymes
• This enzymatic function would be essential if
nucleic acids were the first self-replicating things
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Ribozyme from
Tetrahymena
themophila: a selfsplicing intron between
adjacent rRNA genes
(Fig. 16.2 a)
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The catalysis
performed by the
Tetrahymena
ribozyme in vitro
(Fig. 16.2 b)
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The case for an RNA-based system as an
early life form
• Existence of catalytic RNA
• RNA is a core component of the apparatus for translating
genetic information into proteins – rRNA a component of
ribosomes (probably the component that actually catalyzes
protein synthesis), and tRNA “adapters” also required for
protein synthesis
• Ribonucleoside triphosphates (ATP, GTP) are the basic
energy currency of all cells and are components of
electron-transfer cofactors such as NAD (nicotinamide
adenine dinucleotide) and FAD (flavin adenine
dinucleotide)
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Can RNA evolve? – experimental evolution of RNA
(Beaudry and Joyce 1992)
• Select for the
ability of
Tetrahymena
ribozyme to catalye
the cutting of a
DNA
oligonucleotide and
attachment of a
fragment to its 3’
end
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Test tube
evolution
of RNA
(Beaudry
and Joyce
1992) (Fig.
16.4)
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Can RNA evolve? – experimental evolution of RNA
(Beaudry and Joyce 1992)
• Experiment was seeded with a large population of randomly mutated
ribozymes
• After 10 “generations” the catalytic ability of the average RNA in the
population had improved by a factor of 30
• Most of the improvement in catalytic ability was attributable to
mutations at 4 locations
• Many additional experiments with natural and synthetic RNA have
produced ribozymes that can catalyze reactions such as
phosphorylation, peptide bond formation, and carbon-carbon bond
formation.
• BUT, a crucial piece is missing from the
experiment that we have just described – selfreplication
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Genotypic changes in an evolving RNA population
(Beaudry and Joyce 1992) (Fig. 16.5b)
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Toward self-replicating RNA molecules
• So far, we do not have a self-replicating RNA
molecule (or a self-replicating system of RNA
molecules)
• If we can produce such a thing (perhaps by
selective “breeding” experiments in the
laboratory) then, by one definition at least, we will
have succeeding in creating life (although
obviously not complex cells)
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Laboratory evolution of the ability of catalyze the
joining of adjacent nucleotides (phosphoester bond)
(Bartel and Szostak 1993)
• Variable population of synthetic RNA molecules selected
for ability to catalyze joining of nucleotides
• This is not self-replication, but a necessary function of a
self-replicating RNA molecule
• Experiment still depends on the use of replicating enzymes
to “reproduce” the “successful” RNA molecules after each
“generation”
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Test-tube selection scheme for identifying ribozymes that can
link nucleotides (Bartel and Szostak 1993) (Fig. 16.6 a,b)
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Test-tube selection scheme for identifying ribozymes that can
link nucleotides (Bartel and Szostak 1993) (Fig. 16.6 c,d)
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Test-tube selection scheme for identifying ribozymes that can
link nucleotides (Bartel and Szostak 1993) (Fig. 16.6 e)
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Evolution of
catalytic ability in
a laboratory
population of
ribozymes (Bartel
and Szostak 1993)
( Fig. 16.7)
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RNA world – summary
• RNA molecules possess at least some of the necessary
properties of living systems
– the sequence of nucleotides provides a heritable information storage
mechanism (= genotype)
– Catalytic ability is a variable, heritable phenotype upon which
selection can act
• Natural or synthetic ribozymes possess a variety of
enzymatic activities, including the ability to join
nucleotides together to make short (40 - 50 bp)
polynucleotide strands
• However, so far, no one has succeeded in producing an
RNA molecule that can copy itself
• Even if that is achieved, it still leaves the question of how
the first RNA molecules were made
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Pre-biotic synthesis of organic molecules:
the Miller – Urey experiments (1953)
• Water vapor + methane + ammonia + hydrogen +
electric spark = amino acids (glycine, alanine)
• Similar experiments by others have yielded other
organic compounds, including nitrogenous bases
(from ammonia and hydrogen cyanide) and ribose
(from formaldehyde)
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The Oparin – Haldane model (Fig. 16.12):
“the prebiotic soup”
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Criticisms of Miller – Urey
and Oparin – Haldane
• Earth’s early atmosphere may not have been composed of
methane and ammonia, but rather carbon dioxide and
nitrogen, which would not have been favorable for
formation of the necessary organic molecules (although
aldehydes could be formed from carbon dioxide)
• Formation and stabilization of polymers of basic buiding
blocks (such as amino acids) in the aqueous prebiotic soup
also appears to present difficulties (mineral “scaffolding”?)
• Still a long way from biological polymers to “cells”
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Extra-terrestrial origins?
• Meteorites are sources of amino acids, at least some of
which survive impact
• The Panspermia hypothesis
– Life originated elsewhere in the solar system and was carried here
on meteorites that originated from other planets or moons, or
possibly life originated outside the solar system
– McKay et al. (1996): meteroite from Mars contained globules of
carbonate + magnetite, iron sulfide, and polycyclic aromatic
hydrocarbons: and a suggestion of microfossils that resemble
bacteria
– Many (most?) are not convinced that the Martian rock provides
evidence of life – the compounds that were present can also be
formed by abiotic processes
• In any event, the Panspermia hypotheis merely shifts the
problem of the origin of life to somewhere else at some
other time
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When was life first present on Earth?
• Radiometric dating of meteorites suggests that the solar
system, including Earth, is about 4.5 to 4.6 billion years
old
• Sedimentary rocks from Greenland, and dated at 3.7 billion
years, contain microscopic graphite globules that have a
12C/13C isotopic ratio that is characteristic of molecules
produced by biological processes
• This may be about the oldest evidence of life that we are
likely to find, because conditions much before that might
have been unsuitable for life, or would have obliterated
earlier origins of life
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The history of large impacts on Earth and Moon
(Sleep et al. 1989) (Fig. 16.11)
Red boxes represent lunar
impacts; blue boxes
terrestrial impacts (some of
which are hypothetical.
Dashed line represents
impact energy sufficient to
vaporize the global ocean.
A = Archaean spherule
beds; V = Vredevort; S =
Sudbury; M =
Manicougan; K/T =
Cretaceous-Tertiary impact
crater (Yucatan)
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What was the most recent common ancestor
of all extant organisms?
• Regardless of the origin of organic molecules, and
whether or not an RNA world was an intermediate
step in the evolution of life, the evidence that all
present day life forms share a common ancestor is
compelling
• All life forms (except some viruses) use DNA and
proteins, and all use them in the same way (same
20 amino acids, same genetic code)
• The oldest cellular fossils (which resemble
bacteria) are 3.4 billion years old
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The phylogeny of everything
• Carl Woese (and others)
• We need a highly conserved molecule that has
recognizable similarities across all life forms
• Small subunit ribosomal RNA
–
–
–
–
all organisms have ribosomes
all use ribosomes in the same way (translation)
all ribosomes are composed of RNA + protein
all ribosomes have similar structure, being composed of
small and large subunits
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Small-subunit rRNA phylogeny (Woese 1996) (Fig. 16.18):
Three-domain classification
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The tree of life – old style (Fig. 16.17):
five-kingdom classification
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Three-domain classification system:
Bacteria, Archaea, Eucarya
• Archaea (archaebacteria) more closely related to
eukaryotes than they are to “true” Bacteria
• Archaea composed of two (or three) kingdoms
• Protista must be abandoned as a kingdom
(paraphyletic) or must include animals, plants, and
fungi.
• Animals, plants, and fungi do appear as natural,
monophyletic groups (with removal of slime
molds from fungi)
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What was the most recent common ancestor like?
• Highly evolved and biologically sophisticated –
perhaps similar to modern bacteria
– All living organisms store genetic information as DNA
and have similar transcription and translation
machinery
– DNA polymerases are relatively similar across domains
– All organisms have DNA-dependent RNA polymerases
that show strong similarities across all domains
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Different genes give different universal
phylogenies – 1 (Fig. 16.22 a,b)
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Different genes give different universal
phylogenies – 2 (Fig. 16.22 c,d)
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Horizontal gene transfer
• Inconsistencies among genes for the universal
phylogeny have led to the suggestion that taxa
have exchanged genes horizontally
• Bacteria are known to be able to take up DNA
from their environment and to incorporate that
DNA into their genomes (transformation, etc.)
• 18% of E. coli genes estimated to have arrived by
horizontal gene transfer in last 100 million years
(Lawrence and Ochman 1998)
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Evidence for horizontal gene transfer of the HMGCoA
reductase gene into an archaean (Doolittle and Lodgson 1998)
(Fig. 16.23)
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The cenancestor was not a single species, but
a community (Fig. 16.26)
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The latest possible date for the root of
the tree of life
• Oldest known probable eukaryotic fossils (algae)
are 1.85 – 2.1 billion years old
• Fossil cyanobacteria also suggest that the root is
more than 2 billion years old
• The most recent date for the root of the tree of all
living organisms is between 3.4 and 2 billion years
ago
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The origin of mitochondria and chloroplasts
• The mitochondria and chloroplasts of eukaryotic
cell have their own genomes
• Analysis of small-subunit rRNA genes suggests
that both organelles are derived from bacteria
which have become obligate endosymbionts
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Placement of mitochondria and chloroplasts on the universal
tree based on small-subunit rRNA genes
(Giovannoni et al. 1988) (Fig. 16.30)
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