TuTh

1
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
2
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
3
Science fiction, junk DNA, human uniqueness,
reproduction, evolution and disease Mapping
the Eukaryotic Retrome
4
Retroid Agents
Retroviruses, retrotransposons,
pararetroviruses, retroposons, retroplasmids,
retrointrons, and retrons




reverse transcriptase mediated replication or
transposition
RNA viruses e.g., Ebola, rabies, influenza, polio
All cellular systems most DNA Viruses
RNA
DNA
Replication by DNA-dependent DNA polymerase
Replication by RNA-dependent RNA Polymerase
transcription
translation
snRNAs, ribozymes tRNA, rRNA

PROTEIN SYNTHESIS
McClure, 2000
5
(No Transcript)
6
The Replication and Transcription Cycle of
Retroid Agents
OR
When is it what?
7
(No Transcript)
8
Schematic Classification of Retroid Agents
I Retroviruses
Exo/Endo Retroviradae /-env
orphan class
II Gypsy-like Retrotransposons
Exo/Endo Metaviridae /-env

Exo/End
plant viruses
Pararetroviruses
Hepadnaviruses
III Copia-like Retrotransposons
Exo/Endo Pseudoviridae /-env

LINES
CIN4
Retroposons
R2Bm
Retrointrons
Group II
Introns
of Plastids
Retroplasmids
Plasmids of Plastids
Eubacteria
and
Archea RTs
Retrons
Telomere
Eukaryotic
elongation RT
host gene
9
These are cryo EM 3D reconstructions of two
classes of yeast Ty virus-like particles, with
icosahedral T numbers of 3 and 4.
10
(No Transcript)
11
(No Transcript)
12
Distribution of Retroid Agents among Eukaryotes,
Eubacteria and Archaea
13
Gene Maps
Phylogenetic Tree based
Gene Maps
on 65 RT sequences
MA
C
NC
retroviruses
HIV-1
orphan class
DIRS-1
C
NC
gypsy-like retrotransposons
17.6
caulimoviruses
NC
CaMV
hepadnaviruses
HBV
NC
copia-like retrotransposons
Copia
C
LIN-H
NC
C
CIN4
C
R2Bm
retroposons


NC
C
I-FAC
INGI
introns
INT-SC1
Group II
plasmids
MAUP
retrons
MX65
TERT
1000
2000
3000
4000
RT reverse transcriptase
RH ribonuclease H

Nucleotides
H-C/IN integrase

PR aspartic acid protease
McClure, 2000
14
Roles of Retroid Agents
Disease Regulation of cellular genes and
reproduction Telomere maintenance Repair of
broken dsDNA Exchange of genetic information
among and between organisms
15
In the late 1980s it was first demonstrated that
various ERVs were regulating various mammalian
genes. Starting in the late 1990s it was
demonstrated human ERVs are active in mammals in
a variety of roles.
HERV expression is involved in human sperm-egg
binding and fusion. HERVs W and FRD encodes the
adhesion proteins, the syncytins, that are
essential to human placental development
HERV-E LTRs are alternate promoters for a
significant portion of all Pleiotrophin
(essential for mature neuron formation and
angiogenesis), endothelin B receptor (required
for fetoplacental circulation) and Midline 1
placental transcripts for a microtubule-associated
protein
HERVs provide RT activity to produce
retrogenes associated with male fertility.
This is a post splicing mRNA amplification
process.
Genome-wide microarray analysis on humans of both
sexes indicate that HERVs, are ubiquitously
expressed at low levels in many tissues, however
various types of HERVs appear up regulated in
skin and liver, and various tissues involved in
reproduction.
Expression of the integrase encoded by a MERV is
integral to maternal mitochondrial inheritance.
16
Function of HERV-W
17
The Mutualism Continuum of Human Retroid Agents
HIV
Endogenous retroviruses
Retroviral LTRs
Endogenous retroviruses
LINEs
TERT
HTLV
Chromosomal repair
Gene regulation
Deadly disease
Disease association
Genetic disease
Reproduction
beneficial symbioant
parasite
commensalism
18
The Software to Map the Eukaryotic Retrome
Genome Parsing Suite (GPS) evolves into a
system for Retroid Agent diSCovery and
anALysis, RASCAL
19
What is the host genomic environment of active
Retroid Agents ?
Predict a potentially functional RT
Predict Retroid genome
Real Chromosome
What roles do Retroid Agents play in disease,
development, reproduction and evolution
throughout the three domains of life?
20
Retroid RT queries
RT
RT
RT
WU-tBLASTn RT queries against Host chromosome
RT
RT
RT
RT
Stage I GPS
Analyze all Raw RT hits
RT
RT
Correct for cross coverage
Correct for redundancy
Compound small hits
Unique RT hits
RT
RT
RT
Analysis for frame shifts and stop codons and
ordered series of motifs
LPQGLFK
..PKK..LDL..LPQG..YADDLL..FLG..FLG..
One stop codon, partial motif
All six motifs of the OSM, no stop codons or
frame shifts
Excises a 14Kb chromosomal segment
inclusive of each RT hit
Stage II GPS
RT
7 kb
7 kb
Compares DNA cutout to query component library in
a RT outward fashion thereby constructing the
Retroid agent genome
RH
3LTR
RT
5LTR
GAG
ENV
Query component library
PRO
IN
Reports results for all RT extensions number of
and identity to all query components, stops
codons, and frame shifts. Segments with all
query components in the correct order are labeled
full length with query as closest relative.
PRO
5LTR
GAG
IN
RH
ENV
3LTR
Full length Retroid agent
RT
Perfect one frame shift one stop codon
full-length Retroid genomes Potentially active
sequences
21
HGD Freeze Date
22
Discovery of 11 new FERVs (fish Endogenous
Retroviruses) without getting wet.
23
MrBayes
New viruses OLERV 1-3 DRERV 1-5 GAERV 1-3
Preliminary observations of consensus trees
generated with a mixed amino acid model and
eight category gamma distribution rate produced
high posterior probabilities with a number of
incorrect internodes even after 100,000s of
iterations and apparent convergence.
24
Align all LTR pairs. Measure Distance (d)
between each pair. Estimate insertion time (t).
t d/2r. Rate (r) neutral evolution
(Tetraodon and Takifugu genuses using 5,802
orthologues).
25
Millions of Years (Log10)
Figure 3
26
Fish genomes
Japanese sardine
304.1
D. Rerio
1700 Mbp
Carp
190.1
Zebrafish
O. Latipes
484.9
1000 Mbp
Medaka
179.7
Bastard halibut
G. aculeatus
191.2
675 Mbp
Three-spined stickleback
155.5
Hilgendorfs saucord
183.3
T.Nigroviridis
385 Mbp
Torafugu
84.8
Green Spotted pufferfish
27

• Eukaryotic Retrome

Fungi
Marsupials
Monotremes
other mammals
Reptiles
Birds
Amphibian
Eutheria
Fish
Insects
Animals
Plants
28
(No Transcript)
29

• The Eukaryotic Retrome

other mammals
erv
Fungi
Marsupials
Monotremes
Birds
Reptiles
primates
Amphibian
LINEs
Fish
Insects
Animals
Plants
30
The McClure Lab
Sean Cleveland, Ph.D. graduate student,
Microbiology Undergraduates Holly Basta,
Microbiology Ted Weatherwax, Microbiology
Alex Busak, Computer Science
Sabindra Katlia, Biotechnology Robert
Frost, Microbiology
Software Engineer Rochelle Clinton
Marcella McClure, P.I. (Marcie)
31
Figure 4. Legacy Workflow. Current workflow of
the GPS system including in-house analytical
scripts (3a-b, c-f) and external methods 2.d
and 3.c.
Figure 5. Web 2.0 Application. The new Web 2.0
Application Architecture of the RASCAL will allow
simpler management of the RASCAL data, more
modular development of new functionality and a
rich user interface incorporating the JBrowse
genomic browser and rich web technologies
including AJAX, RSS, and using data in either XML
or JSON format.
32
(No Transcript)
33
(No Transcript)
34
Predictive features of RASCAL
Viability score

• Translational Read Through Model
• 1) Selection of stop codons and frame shifts as
  regulators of ERV
• polycystronic messages.
• 2) Selection of stop codons and frame shifts as
  regulators of specific ERV genes.

Complementarity Model Networks of ERV
co-expression to overcome inactive genes.
35
Host gene expression network
LTR provider
RT provider
Integrase provider
36
Collaboration McClure, Jacobs and Kececioglu
Labs