Lecture 16. Prokaryotes, Eukaryotes, and the
Tree of Life, rRNA, Constructing Trees.
reading: Chapters 3, 5
Ernst Haeckel
Textbook General Morphology 1866
Traces all of life to Moneren (Monera).
Linear progress from Monera to Man.
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Yet another version of
Haeckel’s tree of life
All eukaryotes descended from
prokaryotes, culminating in man.
Prokaryotes not all that interesting.
Zuckerkandl & Pauling
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Pauling: 1954 Nobel Prize,
nature of the chemical bond
Series of papers in 1962-1965:
Mutations form the basis for disease.
Disease has a molecular basis.
Studying diseases that involve different forms of hemoglobin.
Showed that:
a. if you knew the genetic code, you could trace the mutations
that caused disease
b. there is buried history in protein (or gene) sequences (hold information)
c. approximate time of the existence of an ancestral sequence
d. can infer the probable sequence of the ancestor (AACGTTC)
e. can infer “the lines of descent along which given changes in aminoacid sequence occurred”
Overall Scheme for Constructing a Phylogenetic Tree
time
cells/
culture
phylogeny development of a race
or species
DNA extraction
clone
sequence
tree
reconstruction/inference
algorithm
Thermus thermophilus
GAC-ACGUGGU-AUCCUGUCU-GAAUAU-GGGGGG--ACCA-UCC-U-CCA-AG-GCUA-AAUAC-UC-C-UG
Synechocystis PCC 6301 GAC-ACGUGAA-AUCCUGUCU-GAAGAU-GGGGGG--ACCA-UCC-U-CCA-AG-GCUA-AAUAC-UC-G-UG
Micrococcus luteus
GAC-ACGUGAA-AUCCUGUCU-GAAGAU-CGGGGG--ACCA-CCC-C-CGA-AG-GCUA-AGUAC-UC-C-UU
Flexibacterium sp.
GAC-ACGUGAA-AUCCUGUCU-GAACGU-GGGGGG--ACCA-CCC-U-CCA-AG-GCUA-AGUAC-UC-C-UU
Agrobacterium tumefaciens GAC-ACGUGAA-AUCCUGUUC-GAACAU-GGGGAG--ACCA-CUC-U-CCA-AG-CCUA-AGUAC-UC-G-UG
Escherichia coli
GAC-ACGUGGU-AUCCUGUCU-GAAUAU-GGGGGG--ACCA-UCC-U-CCA-AG-GCUA-AAUAC-UC-C-UG
Pseudomonas cepacia
GAC-ACGUGAA-AUCCUGUCU-GAAGAU-GGGGGG--ACCA-UCC-U-CCA-AG-GCUA-AAUAC-UC-G-UG
Aquifex aeolicus
GAC-ACGUGAA-AUCCUGUCU-GAAGAU-CGGGGG--ACCA-CCC-C-CGA-AG-GCUA-AGUAC-UC-C-UU
Chloroflexus aurantiacus GAC-ACGUGAA-AUCCUGUCU-GAACGU-GGGGGG--ACCA-CCC-U-CCA-AG-GCUA-AGUAC-UC-C-UU
Example How to Construct a Phylogenetic Tree
Count the number of
differences. Correct for
multiple mutations.
Construct a Tree that Best Explains the Distances
Observed
Can also Build a Tree using Cladistics
TAB LE 2
fro g
a llig a to r
du ck
cat
opossum
limb s
4
4
4
4
4
s cal es
N
Y
Y
N
N
a m n io te
N
Y
Y
Y
Y
fe a th e rs
N
N
Y
N
N
cladistics - reconstructing trees using
shared, derived traits
1. chose which taxa
2. tabulate traits
3. identify synapomorphies
= shared derived traits
4. build up a cladogram
= tree showing evolutionary relationships
good introductory resource:
www.ucmp.berkeley.edu
h air
N
N
N
Y
Y
pl ace n ta
N
N
N
Y
N
bl oo d
Co ld
Co ld
Wa rm
Wa rm
Wa rm
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The Importance of Having A Phylogenetic Tree
The Importance of Having A Phylogenetic Tree, cont.
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Tree of Life
Constructed by aligning a gene sequence common to all organisms.
Common gene: ribosomal RNA gene.
Three major lineages - these are called domains.
Root is where the last common ancestor gave rise to the three domains.
Root is placed at the base of the bacterial domain.
Ribosome
Synthesizes Proteins in the Cell
Large complex made of RNA and small proteins
RNA catalyzes the reaction to make proteins
RNAs called ribosomal RNAs
1989: Rooting the Tree of Life
three studies:
Gogarten et al.
Iwabe et al.
Baldauf et al.
ATPases
tRNA synthetases
elongation factors
Archaea are more closely related to Eukaryotes than to Bacteria
At first this was a big surprise - expected Bacteria and
Archaea to be more similar to the exclusion of Eukaryotes
The Bacterial Domain
At least 18 divisions - major lineages.
Some divisions have never been cultured!
Some have unique characteristics (e.g., the Cyanobacteria).
Most lack unique characteristics.
One major group Proteobacteria - have a large variety of different
physiologies
Bacterial tree is not
well resolved at
present
The Bacterial Domain, cont.
Early lineages are hyperthermophiles.
Deinococcus branches somewhat deep.
E. coli is a member of the Proteobacteria, branches late.
Cyanobacteria also branch late.
Bacillus & Clostridium members of the Low G+C Gram Positive Bacteria.
Are several lineages of photosynthetic phyla.
Are Five Phyla Contain
Photosynthetic Taxa:
Green Non-Sulfur Bacteria
Green Sulfur Bacteria
Cyanobacteria
Low G+C Gram Positives
(Heliobacillus)
Proteobacteria
Key Characteristics of Bacteria
1. Cell walls made of a similar polymer (peptidoglycan)
2. Lipids are made of similar compounds (fatty acids with ester linkages)
3. RNA polymerase (enzyme that makes mRNA copies of genes)
made of 4 different proteins (’)
4. Signature sequences tell RNA polymerase where to start making
RNA
5. All proteins begin with a modified amino acid formyl-Methionine
The Archaeal Domain
Two major well-studied phyla are Euryarchaeota and Crenarchaeota.
Two new phyla are Korarchaeota (no pure cultures yet) and
Nanoarchaeota (is a symbiont of a Crenarchaeote). Not clear
where these lineages branch.
Most of the early branches are hyperthermophilic.
Obsidian Pool, Yellowstone,
home of Korarchaeota
Crenarchaeota
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All cultured species are hyperthermophilic.
Many inhabit “extreme environments”:
hyperthermophiles- very high T loving
thermoacidophiles - high T acid loving
Many have short branches - evolve slowly.
terrestrial acidic hot spring
(should, in principle, be good models for early life on Earth)
Great deal of uncultured mesophiles (moderate T loving) everywhere - 30% of
biomass in the open oceans.
Mesophiles have long branches - evolving more rapidly.
Mesophilic lineages are peripheral.
marine hydrothermal vent
red cells are Archaea
green are Bacteria
Euryarchaeota
Physiologically diverse group.
Inhabit many extreme environments:
acidophiles- acid loving
thermoacidophiles
halophiles- salt loving
alkaliphiles- alkaline loving
hyperthermophiles
Many lineages are methanogens - generate methane,
are strict anaerobes (can only grow without O2)
Methanogens found in diverse habitats:
swamps, deep-sea hydrothermal vents,
animal intestines, cow rumen, rice paddies,
oil wells
Key Characteristics of Archaea
1. Cell walls are different than bacteria (pseudopeptidoglycan)
2. Lipids different from bacteria (isoprenoids with ether linkages)
3. RNA polymerase more complex than bacteria 8 or more proteins (eukaryotes have 8-10)
4. RNA polymerase needs “help” from other proteins to begin
making mRNA copies of genes (called transcription factors are similar to eukaryotes)
5. Signature sequences also tell RNA polymerase where to start
making RNA, but are unique (TATA boxes - similar to eukaryotes)
6. All proteins begin with the regular amino acid Methionine
7. The number of ribosomal proteins are different from bacteria.
Archaea and Bacteria Share Many Characteristics
1.
2.
3.
4.
5.
6.
Genes are often linked together in the chromosome
Have circular chromosomes (eukaryotes have linear chromosomes)
Genomes are small (eukaryote genomes are huge)
Both have ribosomes that are small (eukaryotes have larger ribosomes)
Both metabolically diverse (eukaryotes are not)
Lack nucleus
…. many more ….
Eukaryotes
Prokaryotes- lack nucleus/nuclei
often have multiple chromosomes
Eukaryote (“true nucleus”)
(linear chromosomes)
are much more complex
lots more genes
DNA containing organelles (“little organs”)
lots of “junk DNA” in their genes
nucleus
mitochondrion - respiration
were once free-living prokaryotes
chloroplast - photosynthesis
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Eukaryotes are Typically Larger than Prokaryotes
Lecture 17. Why Do You Need to Construct a
Tree for Prokaryotes? Trees as Frameworks
reading: none
Mystery of Enceladus
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Cassini Spacecraft found older terrains
and major fractures on moon Enceladus
Course crystalline ice which will degrade over
time.
Must be < 1000 years old!
Organic compounds found in the fractures.
Must be heated - required T > 100K (-173˚C)
Erupting jets of water observed.
Cause of eruptions not known….
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