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 or LUCC. Lecture 7
9/19/06 Origin of the Genetic Code and
more on LUCC. 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 Mutation continued Lecture 11
10/3/06 Methods Analyzing sequences
rates/patterns. Lecture 12 10/5/06 open
discussion Lecture 13 10/10/06. Molecular
Phylogeny I History, terms, definitions, and
limits. Lecture 14 10/12/06 Molecular
Phylogeny II How to determine a phylogenetic
tree. Lecture 15 10/17/06 Molecular
Phylogeny III Bayesian Approaches and Extensions
to Genome Trees. 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
What is Intelligent Design all
about? Lecture 23 11/14/06 Bioethics of
the Human Genome Project/ Introduction to
Bioinformatics. Lecture 24 11/16/06
Examples of in silico research I the RNA
polymerase story. Lecture 25 11/21/06 group
presentation The origin f the thee Domains of
Life3 RNA cells and 3 DNA viruses 11/22-24/06
THANKSGIVING HOLIDAY Lecture 26 11/28/06
group presentation Evolution of Horizontal Gene
Transfer Lecture 27 12/30/06 group
presentation Origin of membranes Lecture 28
12/5/06 group presentation The Evolution of
Archaea Lecture 29 12/7/06 group
presentation Evolution of Bacterial
Extremophiles
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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
• Organismal adaptation
• 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