Title: Lecture 16. Prokaryotes, Eukaryotes, and the Tree of Life, rRNA, Constructing Trees.
1Lecture 16. Prokaryotes, Eukaryotes, and the Tree
of Life, rRNA, Constructing Trees.
reading Chapters 3, 5
2Ernst Haeckel
Textbook General Morphology 1866 Traces all of
life to Moneren (Monera).Linear progress from
Monera to Man.
3Yet another version of Haeckels tree of life
All eukaryotes descended from prokaryotes,
culminating in man. Prokaryotes not all that
interesting.
4Zuckerkandl Pauling
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
amino- acid sequence occurred
5Overall Scheme for Constructing a Phylogenetic
Tree
time
cells/ culture
DNA extraction
phylogeny - development of a race or species
clone
tree reconstruction/inference algorithm
sequence
Thermus thermophilus GAC-ACGUGGU-AUCCUGUCU-GA
AUAU-GGGGGG--ACCA-UCC-U-CCA-AG-GCUA-AAUAC-UC-C-UG
Synechocystis PCC 6301 GAC-ACGUGAA-AUCCUGUCU-GA
AGAU-GGGGGG--ACCA-UCC-U-CCA-AG-GCUA-AAUAC-UC-G-UG
Micrococcus luteus GAC-ACGUGAA-AUCCUGUCU-GA
AGAU-CGGGGG--ACCA-CCC-C-CGA-AG-GCUA-AGUAC-UC-C-UU
Flexibacterium sp. GAC-ACGUGAA-AUCCUGUCU-GA
ACGU-GGGGGG--ACCA-CCC-U-CCA-AG-GCUA-AGUAC-UC-C-UU
Agrobacterium tumefaciens GAC-ACGUGAA-AUCCUGUUC-GA
ACAU-GGGGAG--ACCA-CUC-U-CCA-AG-CCUA-AGUAC-UC-G-UG
Escherichia coli GAC-ACGUGGU-AUCCUGUCU-GA
AUAU-GGGGGG--ACCA-UCC-U-CCA-AG-GCUA-AAUAC-UC-C-UG
Pseudomonas cepacia GAC-ACGUGAA-AUCCUGUCU-GA
AGAU-GGGGGG--ACCA-UCC-U-CCA-AG-GCUA-AAUAC-UC-G-UG
Aquifex aeolicus GAC-ACGUGAA-AUCCUGUCU-GA
AGAU-CGGGGG--ACCA-CCC-C-CGA-AG-GCUA-AGUAC-UC-C-UU
Chloroflexus aurantiacus GAC-ACGUGAA-AUCCUGUCU-GA
ACGU-GGGGGG--ACCA-CCC-U-CCA-AG-GCUA-AGUAC-UC-C-UU
6Example How to Construct a Phylogenetic Tree
7Count the number ofdifferences. Correct
formultiple mutations.
8Construct a Tree that Best Explains the Distances
Observed
9Can also Build a Tree using Cladistics
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
10The Importance of Having A Phylogenetic Tree
11The Importance of Having A Phylogenetic Tree,
cont.
12Tree 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.
13Ribosome
Synthesizes Proteins in the Cell Large complex
made of RNA and small proteins RNA catalyzes the
reaction to make proteins RNAs called ribosomal
RNAs
141989 Rooting the Tree of Life
three studies Gogarten et al. ATPases Iwabe et
al. tRNA synthetases Baldauf et al. 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
15The 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
16The 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 GC Gram Positive Bacteria. Are
several lineages of photosynthetic phyla.
Are Five Phyla Contain Photosynthetic Taxa Green
Non-Sulfur Bacteria Green Sulfur
Bacteria Cyanobacteria Low GC Gram Positives
(Heliobacillus) Proteobacteria
17Key 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
18The 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
19Crenarchaeota
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. (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.
terrestrial acidic hot spring
marine hydrothermal vent
red cells are Archaea green are Bacteria
20Euryarchaeota
Physiologically diverse group. Inhabit many
extreme environments acidophiles- acid
loving thermoacidophiles halophiles- salt
loving alkaliphiles- alkaline loving hyperthermo
philes 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
21Key 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.
22Archaea and Bacteria Share Many Characteristics
1. Genes are often linked together in the
chromosome 2. Have circular chromosomes
(eukaryotes have linear chromosomes) 3. Genomes
are small (eukaryote genomes are huge) 4. Both
have ribosomes that are small (eukaryotes have
larger ribosomes) 5. Both metabolically diverse
(eukaryotes are not) 6. Lack nucleus . many
more .
23Eukaryotes
Prokaryotes- lack nucleus/nuclei Eukaryote (true
nucleus) are much more complex DNA containing
organelles (little organs) nucleus mitochondri
on - respiration chloroplast - photosynthesis
often have multiple chromosomes (linear
chromosomes) lots more genes lots of junk DNA
in their genes
were once free-living prokaryotes
24Eukaryotes are Typically Larger than Prokaryotes
25Lecture 17. Why Do You Need to Construct a Tree
for Prokaryotes? Trees as Frameworks
reading none
26Mystery of Enceladus
Cassini Spacecraft found older terrains and
major fractures on moon Enceladus Course
crystalline ice which will degrade
over time. Must be lt 1000 years old! Organic
compounds found in the fractures. Must be heated
- required T gt 100K (-173C) Erupting jets of
water observed. Cause of eruptions not known.