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Fall 2009 MB437/537 3credits Molecular
EvolutionADVANCES IN Molecular Evolution
What ARE THE latest theories on the Origins of
life? What are genome Sequencing
projects Teaching us about evolutionary
Complexity? What are the Bioethical implications
of Your Future Research?
LUCA
From the Big Bang to Bioinformatics and Beyond

• Tu/Th
• 1100 AM - 1215 PM
• LEWIS HALL 110

Teach Evolution! Learn Science!
Professor Marcie McClure marsmcclure_at_gmail.com
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MOLECULAR EVOLUTION MB437
ADVANCES IN MOLECULAR EVOLUTION
MB537   SYLLABUS   Lecture 1 9/1/09
Comments. Organization Introduction Lecture 2
9/3/09 Evolution the Big Picture Lecture
3 9/8/09 The BIG BANG and formation of the
elements necessary for life. Lecture 4
9/10/09 Biogenesis I The primitive earth and
the prebiotic soup. Lecture 5 9/15/09
Biogenesis II Self-assembly, Energetics and the
Protocell. Lecture 6 917/09 Biogenesis III
More on protocelluar formation. Lecture 7
9/22/09 Biogenesis IV Protein or Nucleic Acids
first? RNA or DNA? Lecture 8 9/24/09
The RNA world the three Domains of life and
LUCA or LUCC. Lecture 9
9/29/09 Origin of the Genetic Code and more
on LUCC Lecture 10 10/01/09 Last Day of LUCA
begin Genomes Content and Architecture Chap 8
10/6/09 open
discussion Lecture 11 10/8/09 Mutation
nucleotide substitutions and amino acid
replacements. Chap 1 3 Lecture 12
10/13/09 Methods Analyzing sequences
rates/patterns. Chap 1,
3-4 Lecture 13 10/15/09 Molecular Clock and
Molecular Phylogeny I History Chap 5 Lecture 14
10/20/09 Molecular Phylogeny I terms,
definitions, and limits. Chap 5 Lecture 15
10/22/09 Molecular Phylogeny II Determining
a phylogenetic tree and Bayesian trees Lecture 16
10/27/09 Molecular Phylogeny III The dance of
the Genome and Genome Trees. Lecture 17 10/29/09
Deviation from Tree-like behavior horizontal
transmission of information.
11/3/09 EXAM Lecture 18 11/5/09
Convergent Evolution the antifreeze
story. Lecture 19 11/10/09 Evolution of
Viruses. Lecture 20 11/12/09 Retroid
Agents eukaryotic hosts and disease
states. Lecture 21 11/17/09 Introduction to
Bioinformatics./Do viral RNA polymerases share
ancestry? Lecture 22 11/19/09 Bioethics of the
Human Genome Project Lecture 23 11/24/09 open
discussion 11/25-27/09 THANKSGIVING
HOLIDAY Lecture 24 12/1/09 Death Lecture 25
12/3/09 Prion Lecture 26 12/8/09 Flu Lecture
27 12/9/09 Carbon
BIG BANG PRIMORDIAL SOUP LUCA BASIC
MOLECULAR EVOLUTION ANALYSIS SPECIAL
TOPICS BIOETHICS
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Evolution of the AFGP Gene 1) de novo function 2)
Recruitment of regulatory elements 3) Sequence
convergence
Work of Chris Cheng Dept. of Animal
Biology University of Illinois Urbana-Champaign
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Antarctica
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Arctic
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Demonstration of direct links between

• Environmental conditions

2) Organismal adaptation
3) Protein evolution
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Freezing Avoidance in Frigid Marine Environment
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Structural Diversity of Antifreeze Proteins
1. AFGP Antifreeze glycoprotein
1 structural type
2. AFP - Antifreeze peptides
AFP I, II, III, IV AFPP (new)
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AFGP Antifreeze Glycoprotein
(a family of size isoforms)
n 4 to 88
m.w. 2,600 to 56,000 Da
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Antifreeze Peptides

• Type I 3-4 kDa

• Type II 14 kDa

• Type III 7 kDa
• 14 kDa

• Type IV 15 kDa

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Phylogenetic relationship of antifreeze-bearing
fishes
Cheng (1998) Curr Op Genet Develop 8715-720
Antifreeze proteins had evolved independently
multiple times!
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Evolution of anti-freezing ability by

• Analogy AFP is analogous to AFGP

2) Recruitment Tyrpsinogen as a precursor to AFPP
3) De novo generation of the AFGP glycopeptide
repeat
4) Convergence evolution of the the glycopeptide
repeat
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Where did antifreezes come from and how did they
evolve?

• Evolutionary Origin
• Molecular mechanism of new gene genesis

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Evolution of anti-freezing ability by
Most Protein Coding Genes Evolved
from Pre-existing Genes
New Gene/ New Function evolutionary ancestry reco
gnizable by sequence similarity
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Type III AFP of eel pouts evolved from C-terminus
of Sialic Acid Synthase
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Antifreeze Peptide
Evolutionary Precursor/Homolog
Evolutionary Mechanism
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Antifreeze Glycoprotein
Evolutionary Precursor/Homolog
Evolutionary Mechanism
Trypsinogen-like serine protease (TLP)
Antarctic Notothenioid AFGP
Recruitment of TLP gene segments and de
novo amplification of 9-nt ThrAlaAla coding
element
?? (not TLP)
Northern and Arctic Cod AFGP
???
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AFGP in Antarctic Notothenioid Fishes
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An AFGP polyprotein gene from D. mawsoni
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Processing of notothenioid AFGP polyprotein
AFGP polyprotein
Chymotrypsin like protease
LNF
FNF
LIF
LNF
carboxypeptidase
Mature AFGP molecules
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Clue to evolutionary ancestry Sequence
similarity to front and tail ends of TLP
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TLP and AFGP Coding/Protein Sequences Entirely
Differernt !
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Chen et al (1997) PNAS 943811-3816
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The smoking gun.
A chimera gene of AFGP and TLP in todays
notothenioid fish genome
Cheng Chen (1999) Nature 40 443-444
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Now why do we think that convergence has
occurred when comparing the Antarctic and
Arctic fish glycopeptide repeat?
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AFGP in Northern Gadids (Cods)
Polar cod B. saida
Saffron cod E. gracilis
Atlantic cod G. morhua
Greenland cod G. ogac
Antarctic notothenioid
AAT-AAT-PAT-AAT-PAR-AAT-AAT-etc
Northern cod
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An AFGP polyprotein gene from polar cod B. saida
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Processing of Cod AFGP Polyprotein
AFGP polyprotein
Trypsin-like protease
R
RAAR
R
R

K
K
K
K
Mature AFGP molecules
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Cod and Notothenioid AFGP Genes Evolved
Independently
Arctic cod AFGP gene
Notothenioid AFGP gene
Signal Peptides Different
Cod AFGP gene Sequence Unrelated to TLP Sequence
Spacers and Processing of Polyprotein Different
Gene Structures Not Conserved
(ThrAlaAla)n Coding Sequence Different
Chen et al (1997) PNAS 943485-3487
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Evolutionary Origin and Mechanism of Cod AFGP
Gene ??

• Problem No similar sequence in the data base
  to
• infer ancestry

• Alternate approach Examine cod genomes
  directly
• for possible ancestral coding elements

• Hypothesis Evolutionary mechanism analogous
  to Notothenioid AFGP gene

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Hypothesis Present in cod genome ancillary 5
and 3 flanking sequences, and a rudimentary
(ThrAlaAla) coding element
Expectation DNA fragments in cods genomes that
will hybridize to 5 and 3 flanking sequence
probes but not (ThrAlaAla)n cds
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Northern Cods Evolved their AFGP gene From Junk
DNA !?
D-box duplication