BASIC OUTLINE OF CLASS

1
BASIC OUTLINE OF CLASS

• 1) Speculation and research on the origin of
  life.
• 2) The RNA world as an intermediary to the DNA
  world generalities, history and current
• A) What was the RNA world like
• B) Current three domain view
• C) LUCA
• 3) Genome Content and Architecture
• 4) Mutation
• 5) Phylogenetic Reconstruction
• A) Term, definitions and limits
• B) How to determine a phylogenetic tree
• C) Improvements and Extensions to Genome Trees
• Deviation from Tree-like Behavior
• Convergent Evolution
• Evolution of Viruses
• Retroid Agents
• 10) Intelligent Design
• 11) Bioethics/Bioinformatics
• 12) Do viral RNA polymerases share ancestry?

2
HIV evolves via point mutation AND recombination
in response to the environment of its host. Can
the host evolve away from HIV?
3
While the immune system naturally drives the
evolution to the ENV gene, AIDs therapies
artificially drives the evolution of the other
genes
4
The Mutualism Continuum of Retroid Agents
HIV
Endogenous retroviruses
Retroviral LTRs
Endogenous retroviruses
LINEs
TERT
HTLV
Cellular promoters
AIDS
Human T-cell leukemia
Chromosomal repair
Gene regulation
Deadly disease
Disease association
Genetic disease
Reproduction
beneficial symbioant
parasite
commensalism
5
Science fiction, junk DNA, human uniqueness,
reproduction, evolution and disease Mapping
the Eukaryotic Retrome
6
RT Motif Chart for all 30 Probes Probe
I II III IV V VI   LINE ILIPKPGR
D LMNIDAKIL TGTRQGCP SLFADDMIVY RIKYLGIQL
PCSWVGRIN LHERV WPVQKTDGS YAAIDLANA TVLPQGYI
VHYIDDIMLI SVKFLGSSG HISYLGVLF EHERV LPVPKPGTK
FTCLDLKDA TQLPQRFK LQYVDDLLLG QVCYLGFTI
VREFLGAVG FHERV ILPIKKPDG FSVLDFKDF TILHQGFR
LQHEDDLLLC KVSYLGLII LLSFLGLVG WHERV LGVQKPNRQ
FTVLDLQDA TILPQGFR SVGVDDLLLA SQQYLGLKL
LRGFLGVIG FRDHERV ILTVKKTNG FSVLDFKNF TVLPQGFR
LQYMDDLLIC AIQYLGIIM FAFLGITR SHERV WPVRKPDGT
HFVVDLANA TMLPQGYV FHYIDDIMIL SAKLLGVIW
FVGFLGYQ RHERV NLSGKKQYP FTVLDLKDA TVLPQGFK
LQYVDDLLIS TIEYLGFLL LKGFLGMAG T47DHERV ILPVKKSDG
FTVIDLKVD TVLPQGFT LQYMDDLLIS EVKYLGHLI
LRKFLGLVT KHERV FVIQKKSGK LIIIDLKDC KVLPQGML
IHCIDDILCA PFHYLGMQI FQKLLGDIN IHERV ILPVKKSDG
FTVIDLKDA TVLPQGFM LQYVDDILIS KVKYLGRLI
LRKFLGLVG HHERV LPVQKPDKS YSVLDLKDG TVLPQGFR
IQYIDELLLC SVTYLGIIL LLSFLGMVG FMuLV LPVKKPGTN
YTVLDLKDA TRLPQGFK LQYVDDLLLA QVKYLGYLL
LREFLGTAG HTLV1 FPVKKANGT LQTIDLKDA RVLPQGFK
LQYMDDILLA TIKFLGQII LQALLGEIQ SRV2 FVIKKKSGK
KIVIDLKDC KVLPQGMA IHYMDDILIA PYTYLGFQI
FQKLLGDIN Snakehead WPVGKPDGS YSSLDISNG TRLPQGFH
LQYVDDILLM QVQYLGVNV LRSALGLFN Spuma YPVPKPDGR
KTTLDLANG TRLPQGFL QVYVDDIYLS TVEFLGFNI
LQSILGLLN FIV FAIKKKSGK VTVLDIGDA CSLPQGWI
YQYMDDIYIG PYTWMGYEL LQKLAGKIN HIV1 FAIKKKDST
VTVLDVGDA NVLPQGWK YQYMDDLYVG PFLWMGYEL
IQKLVGKLN Dirs FTVPKPGTN MVKLDIKKA KTMPFGLS
IAYLDDLLIV SITFLGLQI PRKLAGLKG Gypsy VLVPKKDGT
FTTLDLHSG TVMPFGLV NVYLDDILIF ETEFLGYSI
AQRFLGMIN Caulimo KRRGKKRMV FSSFDCKSG NVVPFGLK
CVYVDDILVF KINFLGLEI LQRFLGILT Badna EVAQKPRIV
FSKFDLKAG NVCPFGIA LLYIDDILIA EVEYLGVEI
LQAYLGLLN HBV FLVDKNPHN WLSLDVSAA RKIPMGVG
FSYMDDVVLG SLNFMGYVI IVGLLGFAA Copia WTITKRPEN
KYQIDYEET MRLPQGIS LLYVDDVVIA IKHFIGIRI
CRSLIGCLM Intron VGGEKGPYS TGRIDDQEN GLTPKTEF
VRYADDLLLG TVEFPGMVI KFRNLGNSI Retron TVEKKGPEK
ILNIDLEDF NLLPQGAP TRYADDLTLS QRKVTGLVI
HHIFCGKSS PMAUP VYIPKANGK FPSVDLAYL NGVPQGAS
IMYADDGILC SVKFLGLEF YIQVLGYLP Archaea IEIPKKSGG
LLEFDIKGL KGTPQGGV ERYADDSVIH KFDFLGYTF
WVNYYGLFY HTERT RFIPKPDGL FVKVDVTGA QGIPQGSI
LRLVDDFLLV EDEALGGTA RRKLFGVLR
7
RNA-dependent DNA Polymerase
Reverse Transcriptase
Ribonuclease H
1 2 3 4
5 6
1 2 3 4
P
D
K
D E D





NX
D
3




fingers
palm
fingers
palm
thumb
connection
Aspartic Acid Protease
1 2 3
1 2 3
DTG G ILG
DTG G ILG
Integrase
1 2 3 4
1 2 3 4
D D E
Hx
H CX
C
Hx
H CX
C
D D E
4
2
4
2
zinc-binding
core
DNA-binding
zinc-binding
core
DNA-binding




8
Retroid Agents
Retroviruses, retrotransposons,
pararetroviruses, retroposons, retroplasmids,
retrointrons, and retrons




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

PROTEIN SYNTHESIS
McClure, 2000
9
Distribution of Retroid Agents among Eukaryotes
and Eubacteria
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The Replication and Transcription Cycle of
Retroid Agents
OR
When is it what?
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Gene Maps
Phylogenetic Tree based
Gene Maps
on 65 RT sequences
MA
C
NC
retroviruses
env
HIV-1
orphan class
DIRS-1
C
NC
gypsy-like retrotransposons
17.6
env???
NC
CaMV
caulimoviruses
hepadnaviruses
HBV
NC
copia-like retrotransposons
Copia
env???
C
LIN-H
NC
C
CIN4
C
R2Bm


NC
retroposons
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, 2006
15
These are cryo EM 3D reconstructions of two
classes of yeast Ty virus-like particles, with
icosahedral T numbers of 3 and 4.
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Roles of Retroid Agents
1) Disease a) retroviruses 1) exogenous
infectious HIV HTLV 2) endogenous
associations breast cancer, testicular tumors,
insulin dependent diabetes, multiple
sclerosis, rheumatoid arthritis,
schizophrenia and systemic lupus erythematosus
b) LINEs insertional mutagenesis 1)
Hemophilia A 2) muscular dystrophies Duchenne
and Fukuyama- congenital type 3) X-linked
disorders Alport Syndrome-Diffuse
Leiomyomatosis and Chronic Granulomatous Disease
2) Regulation of cellular genes and
reproduction 3) Telomere maintenance 4) Repair
of broken dsDNA 5) Exchange of genetic
information among and between organisms
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Roles in Humans
Retroviruses

• Exogenous infections HIV HTLV
• Endogenous associations breast cancer,
  testicular tumors, multiple sclerosis,
  rheumatoid arthritis, schizophrenia and systemic
  lupus erythematosus
• Regulation of cellular genes and reproduction

Retroposons
1) LINEs insertional mutagenesis 1) Hemophilia
A 2) muscular dystrophies Duchenne and
Fukuyama- congenital type 3) X-linked
disorders Alport Syndrome-Diffuse
Leiomyomatosis and Chronic Granulomatous Disease
2) Replication system for Alu sequences
20
Function of HERV-W
21
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
NC
CaMV
caulimoviruses
hepadnaviruses
HBV
NC
copia-like retrotransposons
Copia
C
LIN-H
NC
C
CIN4
C
R2Bm


NC
retroposons
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
22
The Software to Map the Eukaryotic Retrome
23
What is the host genomic environment of active
Retroid Agents ?
Predicted functional RT
Predicted Retroid genome
Real Chromosome
What roles do Retroid Agents play in disease,
development, reproduction and evolution through
out the three domains of life?
24
Genome Parsing Suite (GPS)

• The Stage I
• 1) WU-tBLASTn RT queries through database
• 2) Raw hits sorted by chromosome and direction
• 3) Remove WU-tBLASTn redundancy
• 4) Compound small hits likely to be from one gene
• 5) Remove false positives due to query
  cross-coverage
• 6) Quality assessment of unique RT hits motifs,
  perfect, 1F/S, etc.

Excise 14kb DNA centered on potential RT

• The Stage 2
• 1) WU-tBLASTn each gene component through 14kb
  DNA databases
• 2) Raw hits for each component sorted by contig
  and direction
• 3) Remove WU-tBLASTn redundancy
• 4) Compound small hits likely to be from one gene
• 5) Build each Retroid genome-- using the
  RT-outward approach
• 6) Quality assessment of potential Retroid
  genomes presence of components, stop-codons,
  frame-shifts and percent identity to each query
  component

25
Query component gene maps
ARCHAEA BABAR BARTHEZ2 DEA1 DEWADR1 DREGG1 ERV2_Te
t ERV3_Tet ERV4_Tet FTERT KENOTN1 KIBIDR1 KIBIDR2
KOSHITN1 MAUI
RT
GAG APE UNK RT TE RH
MUTSUDR3
APE RT
R2DR
5UTR GAG RT EN 3UTR
5LTR GAG PRO UNK RT RH IN 3LTR
RETRON
RT
RT RH IN
REX1
APE RT
5UTR GAG APE UNK RT TE RH 3UTR
APE RT
REX3
5LTR GAG PRO IN UNK RT RH 3LTR
UNK RT EN
REX6
GAG PRO RT TE RH IN ENV
RT RH IN
RODIN
PRO UNK RT TE RH IN
SR2
5UTR APE UN RT 3UTR
PRO UNK RT TE RH IN
5LTR GAG PRO RT RH IN 3LTR
SUSHI-ICHI
CARB RT
SUZU
5LTR GAG PRO UNK RT RH IN 3 LTR
GAG APE UNK RT RH
SWIMMER1
5UTR APE UTR UNK RT TE RH 3UTR
5UTR GAG APE UNK RT TE RH 3UTR
5LTR GAG UN RT RH UNK 3UTR
TNDIRS1
5UTR GAG APE UNK RT TE RH 3UTR
5UTR UNK RT EN 3UTR
5UTR GAG APE UNK RT TE RH 3UTR
ZEBULON
5LTR UTR GAG PRO UNK RT UNK2 IN UNK3 ENV 3LTR
5UTR GAG APE RT 3UTR
ZFERV
26
Genome Parsing Suite
RT Query
14 Kb cutout
Assembled Chromosome
RT
KKPIDLLPQGYMDDLYLGFLG
99ID to LINE RT
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Figure 1 Gene products of two common Retroid
agents found in the human genome. A. The Human
Endogenous Retrovirus (HERV) is bounded by two
long terminal repeats (5 and 3 LTRs), with
three major genes GAG encodes proteins essential
for ribonuclear protein complex formation and
capsid assembly POL which encodes the enzymatic
core of the virus including protease (Pr),
Reverse Transcriptase (RT), the tether (T) which
connects the RT and the Ribonuclease H (RH)
domains, and the Integrase (IN) and ENV which
encodes the membrane proteins necessary for
exogenous particle formation. B. The LINE agent
contains many of the same components as a
retrovirus, but lacks LTRs, GAG and ENV, and has
a reduced enzymatic core that includes an
apurinic-apyrimidinic endonuclease (APE) instead
of the IN. A Leucine zipper protein (LZ) is found
in ORF I, and the enzymatic core in ORF II. UN is
a conserved region of unknown function. LINEs
are bounded by untranslated regions (UTRs) that
encode a promoter (P) found in the 5'UTR and a
polyadenylation signal and poly A tail (A(n))
found near the 3' UTR. Both agents are flanked
Target Site Duplications (TSDs), which are 7-21
base host genomic repeats that are hallmarks of
integration of a reverse transcribed DNA.
29
96702 LINEs

RT hits is from 22-250 amino acids

Endogenous retroviruses
Exogenous retroviruses
ParaRetro viruses
?
Retro Trans posons

Retroposons
?
30
Potentially active Retroid agents include perfect
genomes as well as those with one stop-codon or
frame-shift. Many expressed Retroid agents are
known to use translational recoding to correct
one mutational error. There are no potentially
active Retroid Agents in Chimp.
31

• Upgrades to GPS code
• Recombination
• Complementation
• Translational recoding
• Low frequency signals

32
Crystal Hepp Thurs. 315 COOR 74
Holly Basta Fri. 115 COOR 120
Tara Swope Sat. 945 Coor 174
33
The Mutualism Continuum of Retroid Agents
HIV
Endogenous retroviruses
Retroviral LTRs
Endogenous retroviruses
LINEs
TERT
HTLV
Cellular promoters
AIDS
Human T-cell leukemia
Chromosomal repair
Gene regulation
Deadly disease
Disease association
Genetic disease
Reproduction
beneficial symbioant
parasite
commensalism