Download Is there a universal tree of life?

Origins
“There is grandeur in this view of
life, with its several powers, having
been originally breathed into a few
forms or into one; and that, whilst
this planet has gone cycling on
according to the fixed law of gravity,
from so simple a beginning endless
forms most beautiful and most
wonderful have been, and are being,
evolved.”
Only figure in Origins of Species
First depiction of a “tree of life”
Concluding sentence in Darwin’s Origin of
Species
Is there a universal tree of life?
Darwin’s appreciation of the scale of geologic time was key to his theory
Geologists place the beginning of Earth as ~4.55 Bya
Origin of
the earth
4
3
2
Billions of years ago (Bya)
1
Now!
Life arose in the ancient oceans ~ 4 billions years ago
But where? Many possibilities….
Hydrothermal vents?
Energy barriers had to be overcome
Life requires a continual input of energy!
Tidal pools?
Clays may act as catalysts
Miller-Urey experiment (1953)
Objective: to determine if
biomolecules could be generated
from simple compounds in a
mixture of gases designed to
simulate a primitive reducing
atmosphere
Collect products, including amino
acids, nucleotides, sugars, lipids
Chemical origins of life
http://www.pbs.org/wgbh/nova/evolution/origins-life.html
What are the requirements for life?
Life requires:
We accept the cell as the fundamental unit of life
“I took a good clear piece of cork, and
with a Pen-knife sharpen’d keen as a
Razor, I cut a piece of it off, and….then
examining it with a Microscope, me
thought I could perceive it to appear a
little porous…much like a Honeycomb”
Latin “cellulae” means “little rooms”
from Robert Hooke’s Micrographia
How did the first cell(s) form and how long did it take?
Interior of the cell is separated from the environment,
allowing complex process to evolve
Proto-cell has an aqueous interior
with RNA
Surrounded by a lipid shell
(membrane) that isolates it from
the environment
From “The Origins of Life on Earth” by Alonso Ricardo and Jack Szostak
Scientific American September, 2009
RNA serves both catalytic and informational functions
Ribozymes catalyze reactions
Evolve to catalyze many
different reactions
Eventually able to selfreplicate
Hypothetical sequence of events is based on experiments with
synthetic ribozymes (RNA catalysts)
Metabolism begins
Cells take up nutrients and release waste products
Ribozymes work in sequence and
pathways develop
Proteins appear
Systems of ribozymes begin to translate strings of RNAlike nucleotides into strings of amino acids
Proteins take on a variety of
different catalytic and
structural functions
Proteins diversify
eventually replace ribozymes
for most catalytic reactions
DNA takes on the primary informational role in cells
Enzymes synthesize DNA
DNA is more stable than RNA and
becomes primary genetic material
RNA serves as intermediates in
information transfer
Close to 1 billion years were required for the first life form to emerge
4.5 billion years
~billion years before
life emerged
3.5-3.8 billion years
prokaryotes diversify and some
harvest energy from the sun
Modern day example:
Halobacteria are archaea that thrive in salty environments
Red-purple pigments in membranes capture solar energy and
convert it to ATP
from “The Planet of Bacteria”
by Stephen J. Gould
“Our planet has always been in the "Age of Bacteria," ever since the first fossils—
bacteria, of course—were entombed in rocks more than 3 billion years ago.
On any possible, reasonable or fair criterion, bacteria are—and always have been—
the dominant forms of life on Earth. Our failure to grasp this most evident of
biological facts arises in part from the blindness of our arrogance but also, in large
measure, as an effect of scale. We are so accustomed to viewing phenomena of our
scale—sizes measured in feet and ages in decades—as typical of nature.”
First cells appear and some
become photosynthetic, but
do not produce oxygen
Prokaryotes will be the only life forms
for the next 2 billion years
Origin of
the earth
4
3
2
Billions of years ago (Bya)
1
Now!
Primitive cyanobacteria appear
O2 is a product of photosynthesis
Were they responsible for the great oxygenation event ~2.4 Bya?
Layers of cyanobacteria
and carbonates are
apparent in both
modern and ancient
stromatolites
Shark Bay, Australia
Ancient cyanobacteria were important
in the evolution of modern plants
The rise in atmospheric oxygen sets the stage for eukaryotes
Cells can get bigger!
Cyanobacteria
produce O2
photosynthesis
Origin of
the earth
Great Oxidation
Event!!
First
prokaryotes
4
3
2
Billions of years ago (Bya)
1
Now!
Consult the homework assignment on cell size.
A human skin cell is ~10 times larger than E.coli, a bacterium. Use the
equation for volume to estimate how many bacteria would fit into a skin
cell? (Hint: find the ratio of the volumes)
volume = 4/3πr3
Neutrophil chasing a bacterium
Classic movie filmed in the 1950’s by David Rogers at
Vanderbilt University
Note three kinds of cell:
Human neutrophil
Human red blood cell
Staphylococcus aureus
Energy considerations associated with growth
The eukaryotic cell will need 1000 times more energy than E. coli.
The surface area of the cell membrane must be considered. Cells take
up nutrients through their membranes. Respiratory complexes in the
bacterial cell membrane also generate energy.
If a cell is 10 times larger than another one with the same geometry,
how much more energy will it be able to make?
surface area = 4πr2
Several adaptations occurred during the evolution of eukaryotes
Endosymbiont hypothesis
Uptake of prokaryotes
capable of respiration and
photosynthesis was critical
to the evolution of
multicellular eukaryotes
Eukaryotes
appear
photosynthesis
Origin of
the earth
Cyanobacteria
produce O2
First
prokaryotes
4
3
2
Billions of years ago (Bya)
~1 billion years
to first cell
additional ~1.5-2 billion years to
first eukaryotic cell
1
Now!
Consensus view is consistent with sequences of
ribosomal RNA
eukaryotic evolution involved the symbiosis of
bacteria that gave rise to mitochondria and
chloroplasts
LUCA
Changes in rDNA sequences used to predict evolutionary relationships
What is the smallest number of sequence changes that can account for the data?
Human cells have hundreds of mitochondria
inherited from the egg
Inner membrane of mitochondria contains
proteins involved in energy production –
many infoldings increase surface area for
energy production
Mitochondrial DNA (mtDNA)
circular genome with 37 genes
•small and large rDNA
•22 tRNA genes
•small number inner membrane proteins
protein synthesis is more similar to
prokaryotes
Mitochondrial DNA: A closer look
from DNA Learning Center
What happened to disturb this nice tree?
sequences of other genes did not produce the same
tree structure
both archaeal and bacterial sequences could be found
in the same genome
LUCA
Genome projects suggest complex microbial communities at the root
of the tree
Data with individual genes varies
Lateral transfer of DNA has occurred many times,
particularly in prokaryotes
LUCA is replaced with a community of cells