A brief history of the tree of life
Pre DNA – the tree of life is made by ‘organismal biology’
1960’s – Phylogenetics: biomolecules (DNA and protein) are used
to derive tree of life.
1970’s – The 16S ribosomal tree offers the best picture of the tree
of life
1990’s – The genomic revolution offers to increase the resolution
of tree of life but instead casts the entire concept into jeopardy.
The basal universal phylogenetic tree inferred from
comparative analyses of rRNA sequences
C.R.Woese. “Interpreting the universal phylogenetic tree.”
PNAS (2000), 97:8392-8396
The problem: different molecules can yield different trees
AND may still be telling the truth
Even the sacred of sacreds of phylogenetic taxonomy can be violated:
Gene tree A
Gene tree B
Archae
Bacteria
Gene tree C
Kingdoms are not monophyletic
in gene tree B and C
Evolution by Horizontal Transfer
May be detected in genomic sequences because of the presence of
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Unexpected ranking of sequence similarity among homologs
Unexpected phylogenetic tree topology
Unusual phyletic pattern
Conservation of gene order
Anomalous DNA composition
It has an important role in bacterial diversity
The ability of organisms to absorb DNA from the environment was
illustrated by Avery, McLeod, and McCarthy in 1944.
1944 - Avery, McLeod and McCarthy identify DNA as the
"transforming principle" in pneumococcus type III (the genetic
material).
“Infectious heredity”
Horizontal transfer was first recognized (1950’s) in the resistance
to multiple antibiotics simultaneously transferred from Shigella to
Escherichia coli
Macromolecules
Cell Membrane
DNA
RNA Transcription and Transport
RNA Translation
Proteins
Bacterial (prokaryotic) cell
Animal (eukaryotic) cell
Plant (eukaryotic) cell
1.
2.
3.
4.
5.
6.
Nucleolus
Nucleus
Ribosome
Vesicle
Rough endoplasmic reticulum
Golgi apparatus
7. Cytoskeleton
8. Smooth endoplasmic reticulum
9. Mitochondrion
10. Vacuole
11. Cytosol
12. Lysosome
13. Centriole
SCHEMATIC STRUCTURE OF LIVING EUCARYOTIC CELLS
receptors
channels
CYTOPLASM
Microtubule:
mechanics of cell
division, separation of
chromosomes
molecular motors
MEMBRANE
lysosomes
digestion of
receptors
GOLGI
vesicular
transport
Synthesis
of membrane bound
enzymes
ER
NUCLEUS
ATP
amino
acids
mRNA
Actin filaments,
cellular movement
ribosomes
proteins
~ 20 µm
proteasomes
The cell membrane: an active border
"The plasma membrane is a complex assembly of proteins floating
like loosely anchored ships on a lipid sea" Raven and Johnson, 1992
A tipical phase diagram of a
phospholipid bilayer.
(dimyristoyl-lecitin)
Results of numerical simulations.
The different phases are modeled with
different densities
DNA structure
RNA transcription
RNA transport
RNA translation