MOLECULAR EVOLUTION MB437 and ADVANCES IN MOLECULAR EVOLUTION MB537

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MOLECULAR EVOLUTION MB437 and ADVANCES IN
MOLECULAR EVOLUTION MB537 Marcie McClure, Ph.D.
,mars_at_parvati.msu.montana.edu, 994-7370 Fall,
2006, Tu/Th 1100-1215 Cooley-B2 Lecture 1
8/29/06 Organization Introduction What is
molecular evolution? Lecture 2 8/31/06
The BIG BANG and formation of the elements
necessary for life. Lecture 3 9/5/06
Biogenesis I The primitive earth and the
prebiotic soup. Lecture 4 9/7/06
Biogenesis II Self-assembly, Energetics
and Bioinformational Molecules. Lecture 5
9/12/06 Biogenesis III Protein
or Nucleic Acids first? RNA or DNA? Lecture 6
9/14/06 The RNA world the
three Domains of life and LUCA. Lecture 7
9/19/06 Origin of the Genetic Code and more
on LUCA Lecture 8 9/21/06
Genomes Content and Architecture. Lecture 9
9/26/06 Mutation nucleotide
substitutions and amino acid replacements. Lecture
10 9/28/06 Methods Analyzing sequences
rates/patterns. Lecture 11 10/3/06
open discussion Lecture 12 10/5/06
Molecular Phylogeny I History, terms,
definitions, and limits. Lecture 13 10/10/06.
Molecular Phylogeny II How to determine a
phylogenetic tree. Lecture 14 10/12/06
Molecular Phylogeny III Improvements and
Extensions to Genome Trees. Lecture 15 10/17/06
NEW? Bayesian and HMM Approaches to
plylogenetic reconstruction Lecture 16 10/19/06
Deviation from Tree-like behavior
horizontal transmission of information Lecture 17
10/24/06 open discussion Lecture 18
10/26/06 Convergent Evolution the
antifreeze story. Lecture 19 10/31/06
Evolution of Viruses Lecture 20 11/2/06
Retroid Agents eukaryotic hosts and disease
states. Lecture 21 11/7/06 UNIVERSITY HOLIDAY
Lecture 22 11/9/06 Bioethics of the
Human Genome Project/ Introduction to
Bioinformatics. Lecture 23 11/14/06
Examples of in silico research I the RNA
polymerase story. Lecture 24 11/16/06
Examples of in silico research II the Genome
Parsing Suite finds Retroid Agents. Lecture 25
11/21/06 Protein Disorder predictions
Measles the elegance of in silico and wet
experiments 11/22-24/06 THANKSGIVING
HOLIDAY Lecture 26 11/28/06 Lecture 27
12/30/06 Lecture 28 12/5/06 Lecture 29
12/7/06
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Genomic and Regulatory Features of Archaea Domain
Eubacteria-like 1.) single-circular
chromosomes with some genes in polycistronic
operons in the same order as
Eubacteria 2.) no 5 cap Eukaryotic-like 1.)
N-linked glycoproteins 2.) shared
resistance/sensitivity to antibiotics 3.) lacks
of fmet 4.) lacks any homology or analogue to
the Shine Delgarno sequence 5.) presence of
tRNAs with introns 6.) most importantly,
transcriptional regulation a) DNA-dependent
RNA polymerase (transcriptase) b) the
consensus archaic promoter is similar in
sequence and relative position to that of
the eukarya promoter c) the polymerase
requires eukarya-like transcription factors for
promoter recognition d) one of these
factors uses a TATA box and is essentially
eukarya TFIID.
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• What questions should be answered?
• How and When was RNA transferred to DNA?
• How and When did the genetic code evolve?
• How and When did translation evolve?
• How and When did real cell membranes evolve?
• Where did the nucleus come from?
• How did Eukaryotic compartmentalization occur?

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Table 1 (Forterre, 1997)
Classification of
Universal rRNA and Protein Trees According to

Their Geometry and
Topology
Trees with Archaea, Bacteria, and Eucarya more or
less equidistant 16/18S rRNA 23/28S rRNA leu
tRNA synthetase Ribosomal proteins L15, L30,
L17, S30, S2 Adenylosuccinate synthase
(purA) Histidine I Trees with Archaea more
closely related to Eucarya Membrane ATPase a and
ß subunits (V/F) Elongation factor EF Tu (1a)
and EFG Ribosomal proteins L12, L50, S18 RNA
polymerases Tree with Bacteria more closely
related to Eucarya Malate dehydrogenase Trees
with Bacteria more closely related to
Archaea Citrate synthases ftsZ Trees that do
not yield topology of the three
domains Ribosomal proteins L11, L10, L1, S17
(Archaea paraphyletic) DNA polymerase B (Eucarya
paraphyletic) 5 Topoisomerase I (Bacteria
paraphyletic) Glutamine synthetase (Archaea and
Bacteria paraphyletic) Glyceraldehyde 3-P
dehydrogenase (Bacteria and Eucarya
paraphyletic) Glutamate dehydrogenase (all
domains paraphyletic) Ornithine transcarbamylase
(Archaea in Bacteria) Heat shock protein HSp70
(Archaea in Bacteria) V-ATPase (Archaea in
Bacteria) Topoisomerase II (Archaea in Bacteria)
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The LUCA New Zealand style Eukarya as
ancestral 1998-2000 David Penny and
colleagues
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The LUCA Russian style The minimal gene
set 1999-2003 Eugene Koonin and colleagues
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The LUCA French style Eukarya as
ancestral 1998-2002 Patrick Forterre and Herve
Philiepp
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The LUCA American style LUCA as a
community 2002 Carl Woese and Ford Doolittle
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The LUCA English style LUCA as an
Eubacteria 2001-2002 Tom Cavaler-Smith
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The LUCA Chinese/French style LUCA as an
Archean 2003 Xue and colleagues
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The LUCA American style The Ring of Life 2004
Jim Lake and Maria Riveria
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The latest LUCA New Zealand style The
Irreducible Nature of the Eukaryotic Cell 2006
David Penny and crew
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The lastest LUCA French style Three RNA cells
and Three DNA viruses 2004 Patrick Forterre