Stability and Compensated Pathogenic
Deviations
Fyodor A. Kondrashov
Section of Ecology, Animal Behavior and Evolution
University of California at San Diego
How can we make an elephant from scratch?
giraffe
elephant
TACG
ATGC
ATCG
Common ancestor
giraffe
ATGC
TTGC
TAGC
AACG
ATCC
AAGC
TTCC
AACC
TTCG
AAGG
TAGG
ATGG
ATCG
TTGG
TACC
Common ancestor
elephant
TACG
Ideal World Breeding
Real World Breeding
x
x
Fitness
Genotype
Genotype
MITOMAP
A human mitochondrial genome database
A compendium of polymorphisms and mutations of
the human mitochondrial DNA
Are human pathogenic mutations also pathogenic to closely related
species?
Disease
Symptoms
Chronic Progressive
External Ophthalmoplegia
exercise intolerance, mild bilateral ptosis, limb
weakness, and respiratory chain complex III deficiency,
Leber Hereditary Optic
Neuropathy
mid-life, acute or subacute, painless, central vision loss
leading to central scotoma, mean age onset 27-34
Mitochondrial
Encephalomyopathy
episodic vomiting, seizures, and recurrent cerebral
insults resembling strokes and causing hemiparesis,
hemianopsia, or cortical blindness. 80% of cases
affected patients aged 5 to 15 years
Mitochondrial Myopathy
proximal and subsequently distal muscle fatigability
and weakness at ages 5 to 10 years
mitochondrial
encephalomyopathy
pigmentary retinopathy, dementia, hypoparathyroidism,
and diabetes mellitus. Early childhood onset.
Leigh syndrome
early-onset progressive neurodegenerative disorder
with a characteristic neuropathology consisting of focal,
bilateral lesions in one or more areas of the central
nervous system, including the brain stem, thalamus,
basal ganglia, cerebellum, and spinal cord
Methods.
Genbank
Complete
mammalian
mitochondrial
genomes
Synteny
preserved in most
mammals (except
marsupials)
Phylogeny
information
22 tRNA multiple
alignments with 106
mammals and with
marked CPDs
Pathogenic
mutations
Multiple
alignment
Secondary
structure info
A multiple alignment of primate orthologs for Glycine (G) tRNA.
human
chimpanzee
pygmy chimpanzee
gorilla
orangutan
Sumatran orangutan
hamadryas baboon
Barbary ape
common gibbon
capuchin
ring-tailed lemur
slow loris
western tarsier
actcttttagtataaat--agtaccgttaacttccaattaactagttttgac-aacattcaaaaaagagta
actcttttagtataaGt--agtaccgttaacttccaattaactagttttgac-aacattcaaaaaagagta
actcttttagtataaGc--agtaccgttaacttccaattaactagttttgac-aacattcaaaaaagagta
actcttttagtataatt--agtaccgttaacttccaattaaccagttttggt-agtacccaaaaaagagta
actcttttagtataaGc--agtaccgttaacttccaattaaccagttttgac-aacactcaaaaaagagta
actcttttagtataaac--agtaccgttaacttccaattaactagttttgac-aacGcccaaaaaagagta
actcttttagtataatt--agtacaAttgacttccaatcaatcagctttgac-aatattcaaaaaagagta
actcttttagtataacc--agtacaAttgacttccaatcaatcagttttgac-aacattcaaaaaagagta
actcttttagtataaac--agtactgttaacttccaattaaccagcttcgat-aacGctcgaaaaagagta
attctcttagtataaac--agtacaAttgacttccaattaataggccttgat-aa-acccaagagagaata
attcttttagtatcgacccaatacaAttgacttccaattaattaacttcggtgaa-aaccggaaaagaata
gctcttttagtacaact--agtacaAttgacttccaatcaataggatttggtaaataaccaaaagagagca
gttcctttagtatcaatt-agtacaAttgacttccaatcaattagccctagtacaattctaggaaggaaca
.
*
.
*
*
A multiple alignment of selected mammalian orthologs for Luicine UUR (L1).
human
western tarsier
northern tree shrew
European hare
Egyptian jerboa
Eurasian red squirrel
Madagascar hedgehog
little red flying fox
Japanese house bat
polar bear
Atlantic walrus
greater Indian rhino
narwhal
Indus River dolphin
pig
nine-banded armadillo
aardvark
Asiatic elephant
African elephant
wallaroo
common wombat
platypus
Australian echidna
gttaagatggcagagcccggtaatcgcataaaacttaaaactttacagt-cagaggttcaattcctcttcttaaca
gttaagatggcagagcccggCaattgcataaaacttaaaactttattat-cagaggttcaactcctcttcttaaca
gttaaggtggcagagcccggtcattgcctaaaacttaagattttaAgta-cagaagttcaaatcctctccttaaca
gttaaggtggcagagcccggCaattgcataaaacttaaaactttataat-cagaggttcaactcctctccttaaca
gctaagatggcagagcccggtaattgcaCaagacttaaaccCttgAatc-cagaggttcaactcctcttcttaGca
attaagatggcagagcccggcaattgcataagatttaaaacCttactat-cagaggttcaactcctcttcttaaTa
attaagatggcagagcc-ggtaattgcaCaagacttaaaccCttgctgt-cagaggttcaatCcctcttcttaaTa
gttaggatggcagagcccggCaattgcataaaacttaagcttttataat-cagaggttcaactcctcttcctaaca
gttaaagtggcagagaccggtaattgcataaaacttaagattttagagc-cagaggttcaactcctctctttaaTa
gttagggtggcagagcccggtGattgcataaaacttaaacctttatact-cagaggttcaaatcctctccctaaca
gttagggtg-cagagcccggtaattgcataaaacttaaacttttacccc-cagaggttcaactcctctccctaaTa
gttaggatggcagagcccggtaactgcataaaacttaaacctttataac-cagaggttcaactcctcttcctaaca
gttgggatggcagagtacggCaattgcataaaacttaaacctttatacc-cagaggttcaaatcctcttcccaaca
gttgaggtggcagagtccggCaattgTataaaacttaaacttttacact-cagaggttcaaatcctctccccaaca
attagggtggcagagaccggtaattgcgtaaaacttaaacctttattac-cagaggttcaactcctctccctaaTa
gttaagatggcagagacaggtaattgcataagacttaaacctttattac-cagaggttcaaatcctcttcttaaca
gttaaggtggcagagcccggtaattgcataaaacttaagcttttacaac-cagaggttcaattcctctccttaaca
gttaagatagcaaaaattggtcactgcataaaacttaagcttttactca-cGgaggttcaactcctcttcttaaca
gttaagatagcaaaaactggtcactgcataaaacttaagcttttactca-cGgaggttcaactcctcttcttaaca
attaaggtggcagagcc-ggCaattgcataaaacttaaacctttataat-cagaggttcaaatcctctccttaaTa
attaaggtggcagagca-ggtaattgcataaaacttaagcctttacaac-cagaggttcaaaCcctctccttaaTa
attaaggtgacagagaccggtaattgTgtaaaacttaagcttttatagt-cagaggttcaaatcctctccttaaTa
attaaggtgacagagaccggCaattgTgtaaaacttaagcttttataat-cagaggttcaaatcctctccttaaTa
.
.**. . * * .
.
* . *
*
. *
**
Compensated Pathogenic Deviation (CPD)
Molecular event (substitution or other) that is
present in a wild-type in one species and is pathogenic in
another species.
Compensatory Deviation
Molecular event (substitution or other) that negates
the deleterious effect of a Pathogenic Mutation
Can we say anything about a molecular or structural basis of compensations?
Homo sapiens tRNAAsn
3’
G
U A
A U Acceptor
G C stem
A U
U G
U G
G U
U GA
UACCC
A
A
A
UUG
GUGGG
A CCG
G
U UU
U
A
U TYCU U AG G G U
U
G
G stem/loop
D-stem/
C GU
loop
U A
U A Anticodon
A U stem/loop
G C
C
A
U
A
GU U
5’
Pan troglodytes
(chimpanzee) tRNAAsn
3’
5’
G
A
U
C
U
A
A
U
U
A
Acceptor G
stem
A
G
U
G
U
G
U GA
UACCC
A
A
A
UUG
GUGGG
A CCG
G
U UU
U
A
U TYCU U AG G G U
U
G
stem/loop
G
U
D-stem/
U
A
C
loop
U A G
U A
A U Anticodon
G C stem/loop
C
A
U
A
GU U
Figure 2a
Cynocephalus variegatus
(Malayan flying lemur) tRNALys
3’
C
A
5’ C G Acceptor
A U stem
C U A G
U C A
G C
U AUU C
D-stem/ A G C
CA
C
C
U
U
C
A
A
loop
A U GG A A G
U
AG U CG
UA C
U
AC A G C
A AA G
A
U A
A
U U
G TYCU A A stem/loop
U A
Anticodon A U
stem/loop A U
C G
C
A
U
A
UUU
Figure 2b
C
CG
human
Common ancestor
CA
UG
chimp
UA
Ceratotherium simum
(white rhinoceros) tRNATrp
3’
G
Acceptor A U
G C
stem
A G C U
A U
A U
U A TYCU A stem/loop
A
C
U
UUCA U A
A
A
C AU
UGG
A AGU A A
A
C
C
U
C
U
C AG A C C
C
G
G
UA
A
A
D-stem/
A
A U
loop
C
G C
A G C
G A C Anticodon
C G stem/loop
C
A
U
A
UC A
5’
Figure 2c
Ursus maritimus
(polar bear) tRNASer(UCN)
3’
A
U
A U
A G C U
A U Acceptor
A G U
U
A U stem
G C
A
U
U CA
G
CUUCC
A
G
U GAU A C
G A GGG
G
G
U UC
A
U
G
G U U A UG
TYCC
U
A
C
stem/loop
G U
C C
U
D-stem/ G A U C
G U A G
loop
U A Anticodon
G C stem/loop
G C
C
A
U
A
UGA
5’ G
Figure 2d
Spalax ehrenbergi
(Ehrenberg's mole-rat) tRNAIle
3’
A
5’ A U
G C
Acceptor A U
stem
A U
TYCA U
stem/loop
U C G A
A U
CG A
U
C
U
C
C
U
A
U
A G A GG CA
A G C C UG
U
U
U
A CAGA
A G A C UU
A
A
G
A
U
A
U A
D-stem/
U G A
loop
A U Anticodon
C G stem/loop
U A
U
G
U
A
GAU
Figure 2e
Tamandua tetradactyla
(southern tamandua) tRNAIle
3’
A
5’
A U
G C
Acceptor A U
A U
stem
TYCA U
C stem/loop
U A
A U
C GA A
U
U
U UCU CC
C
A G C C UG
A
G
A
G
G
C
U CA A
U
A AGG A
A GA
U
A
CU
C
A
D-stem/
A U
A
loop
AA
U
G U
U A
A U
C G Anticodon
U A stem/loop
U
G
U
A
GAU
Hyperoodon ampullatus
(northern bottlenose whale) tRNALeu(UUR)
3’
A
G C Acceptor
U A
U A stem
A
G C U
G U
A
U
G C
D-stem/
A
C
G C U
loop
U AA
U
C
U
C
U
C
C
G
CU A
G
A
G
A
C
G
AG A GG
U
U UC
C
G
C UGU
U C TYCG
A
CA
G C stem/loop
A
C
C
U
A
U
U AC
A U
Anticodon A U
stem/loop A U C
A U
C A
C
U
A
A
UA
5’
Figure 2f
Tachyglossus aculeatus
(Australian echidna) tRNALeu(UUR)
3’
5’ A
A U
G U A C
U A Acceptor
A U stem
A U
U
G
C
D-stem/ A
G C U
C
U AA
loop
U
C
U
C
C
G
U
A GA
A
C
G
A G A GG
C
GACA
C
U
U
C
G
U TYCU UGU
G
A stem/loop
C AA
G
A G
C C
U
U
A U A
A U C
A U
Anticodon A U
stem/loop A U C
C
C A
U
G A
UAA
Oryctolagus cuniculus
(rabbit) tRNACys
3’
U
A U
G C
C G
U
C G
C G
A
C
C
U G
G C
C A
A
A
CG UC U
A
G
G
U
C
GC AGC
G G UG
A
U U
A
C
ACA U
UA
A
A
G
A
U
U A
U
U A G
G C
A U
A U
U
A
U
A
GC A
5’
Canis familiaris
(dog) tRNALeu(UUR)
3’
A
G C
U A Acceptor
U A stem
A U
A
G C U
A G C
G C U
G
A
U UA
GG
C
U
C
U
C
C
C
U
A
G
A CG
C
A G A GG C
UU
G
C
C U GC
U TYCG
A
G
UA
A stem/loop
UC
A U AC U
G
D-stem/
A
U
A
loop
A U Anticodon
A U stem/loop
A C
C
C A
U
A
UAA
5’
Wittenhagen, L.M. & Kelley, S.O.,
Nat. Struct. Biol. (2002) and
Trends Biochem. Sci. (2003),
Molecular characteristics of the pathogenic mutations
GC ->
GU
GC pair
destroye
d
8
5
Mechanisms
of
compensatio
n in
mammalian
(primate)
species
AU ->
GU
AU pair
destroyed
7
Mutation in loop
or between
stems:
18
In stem, not
disruptive to WC
pair: 2
Total
12
52
Restoring
Watson-Crick
Interactions
3 (2)
6(2)
9(3)
7(2)
0
25(9)
New WatsonCrick
interaction
1
2(2)
3(2)
2(1)
0
8(4)
0
1
3
0
0
4
1
0
1
0
1
3
2
3(1)
4
2
0
11 (1)
3(1)
0
4 (2)
0
19(14)
26(17)
AU -> GC
Change in
loop length or
sequence
Multiple
interactions
strengthened
or newly
evolved
Compensatio
n unclear
So what?
1) This can be used to study the limits of tRNA
stability in evolution
2) DM incompatibilities are intergenic, not expected
to be revealed in F1 generation
3) Molecular basis of compensatory evolution is
much more varied than has been appreciated
4) Fitness ridges of tRNAs are very epistatic such
that 50% of all substitutions are compensatory
5) Fixation of CPD and/or Compensatory mutations
occurs under positive selection
Polymeropoulos MH, et al., Science, 1997
Usual model of fitness: fitness potential
f(p) = fitness, where p is the fitness potential such that
p = c1a + c2b … + cnn
where cnn is the total fitness contribution of allele (mutation) n
This model cannot describe the evolutionary trajectory of CPDs.
Fitness in colour:
Low fitness
Medium fitness
Neutral case:
(1,0)
(1,1)
CPD
(0,0)
(0,1)
Compensatory
High fitness
Other types of CPD fitness surfaces
(1,0) (1,1)
CPD
(1,0) (1,1)
CPD
(0,0) (0,1)
Compensatory
(1,0) (1,1)
CPD
(0,0) (0,1)
Compensatory
(0,0) (0,1)
Compensatory
(1,0) (1,1)
CPD
(0,0) (0,1)
Compensatory
Figure from DePristo et al. Nat. Genet. Rev. 2005
Fitness:
From DePristo et al. Nat. Genet. Rev. 2005
Fitness
Genotype
Genotype
Acknowledgements
Alexey Kondrashov
Shamil Sunyaev
Andrew Kern
NCBI, NIH
Harvard Medical School
University of California, Santa Cruz
Financial Support
National Science Foundation Graduate Research Fellowship