Download long - David Pollock

Evolution of Proteins and Genomes
Biochemistry and Molecular Genetics
Computational Bioscience Program
Consortium for Comparative Genomics
University of Colorado School of Medicine
[email protected]
www.EvolutionaryGenomics.com
Evolution of Proteins
Jason de Koning
Description
Focus on protein structure, sequence, and
functional evolution
Subjects
structural comparison and prediction, biochemical
adaptation, evolution of protein complexes,
probabilistic methods for detecting patterns of
sequence evolution, effects of population structure on
protein evolution,
lattice and other computational models of protein
evolution, protein folding and energetics,
mutagenesis experiments, directed evolution,
coevolutionary interactions within and between
proteins, and
detection of adaptation, diversifying selection and
functional divergence.
Reconstruction of Ancestral
Function
How do You Understand a New
Protein?
Structural and Functional Studies
Experimental (NMR, X-tallography…)
Computational (structure prediction…)
Comparative Sequence Analysis
Looking at sets of sequences
A common but wrong assumption: sequences are a
random sample from the set of all possible sequences
Mouse:
Rat:
Baboon:
Chimp:
…TLSPGLKIVSNPL…
…TLTPGLKLVSDTL…
…TVSPGLRIVSDGV…
…TISPGLVIVSENL...
Conserved
proline
Variable
“High entropy”
Comparative Sequence Analysis
Looking at sets of sequences
In reality, proteins are related
by evolutionary process
Confounding Effect of Evolution
…TLSKRNPL…
SF
PT
…TLFKRNPL…
…TLSKRNTL…
…TLSKRNT…
…TLFKRNP…
…TLSKRNT…
…TLFKRNP…
…TLFKRNP…
…TLSKRNT…
Confounding Effect of Evolution
…TLSKRNPL…
SF
PT
…TLFKRNPL…
…TLSKRNTL…
…TLSKRNT…
…TLFKRNP…
…TLFKRNP…
…TLSKRNT…
…TLFKRNP…
…TLSKRNT…
Everytime there is an F, there is a P!
Everytime there is an S, there is a T!
Ways to Deal with This…
Most common: Ignorance is Bliss
Some: Try to estimate the extent of the
confounding (Mirny, Atchley)
Remove the confounding (Maxygen)
Include evolution explicitly in the model (Goldstein,
Pollock, Goldman, Thorne, …)
Fitness
Selective
Pressure
Folding
Mouse:
Rat:
Baboon:
Chimp:
Stability
Function
Selection
Stochastic
Realizations
A
B
C
…TLSPGLKIVSNPL…
…TLTPGLKLVSDTL…
…TVSPGLRIVSDGV…
…TISPGLVIVSENL...
Understanding
Selective
Pressure
Folding
Mouse:
Rat:
Baboon:
Chimp:
Stability
Function
Data
Model
A
B
C
…TLSPGLKIVSNPL…
…TLTPGLKLVSDTL…
…TVSPGLRIVSDGV…
…TISPGLVIVSENL...
Purines
Pyrimidines
DNA
What does DNA do?
Replication
Translation
Folding
mRNA
DNA
Protein
Protein
Function
Mutations result in
genetic variation
Selective
Pressure
Genetic changes
…UGUACAAAG…
Substitution
Insertion
Deletion
…UGUAUAAAG… …UGUAAAAG… …UGUUACAAAG…
Substitutions Can Be:
Purines:
Transitions
A
G
Transversions
Pyrimidines:
C
T
Substitutions in coding regions can be:
Cys Arg Lys
UGU/AGA/AAG
Silent
Nonsense
Missense
UGU/CGA/AAG
Cys Arg Lys
UGU/GGA/AAG
Cys Gly Lys
First position: 4% of all changes silent
Second position: no changes silent
Third position: 70% of all changes silent (wobble position)
UGU/UGA/AAG
Cys STOP Lys
Homologous crossover
Uneven crossover leading to gene deletion and duplication
Gene conversion
Fate of a duplicated gene
Keep on doing whatever it originally was
doing
Lose ability to do anything
(become a pseudogene)
Learn to do something new
(neofunctionalization)
Split old functions among new genes
(subfunctionalization)
Homologies
Gene
duplication
a Hemoglobin
b Hemoglobin
Speciation
Mouse
a Hb
Rat
a Hb
Paralogs
Mouse
b Hb
Orthologs
Rat
b Hb
Initial Population
Mistakes are Made
Elimination
Polymorphism
Fixation
Selection
Differences in fitness (capacity for fertile offspring)
1 gene
2 alleles (variations), A and B
3 genotypes (diploid organism): AA, AB, BB
Genotype
Fitness
ωAA = 1 (wild type)
ωAB = 1 + SAB
ωBB = 1 + SBB
AA
AB
BB
S > 0 advantageous
S < 0 unfavorable
S ~ 0 neutral
Evolution of Gene Frequencies
q = frequency of B
p = (1-q) = frequency of A
, ,
 population: differential equation for p, q
q(next generation)
= q(this generation) +
pq[psAB + q(sBB-sAB)]
p2 + 2pq(sAB+1) + q2(sBB+1)
Fixation of an Advantageous
Recessive Allele (s=0.01)
Frequency of B
1
0.8
Genotype
AA
AB
BB
0.6
0.4
Fitness Value
1.0
1.0 (recessive)
1.01
0.2
0
0
1000
2000
3000
Generation
4000
5000
Equilibration of an
Overdominant Allele
1
Frequency of B
0.8
0.6
Genotype
0.4
Fitness Value
AA
AB
BB
0.2
1.0
1.02
1.01
0
0
200
400
600
Generation
800
1000
Probability of fixation =
1-e-2s
1-e-2Ns
1
N = 10
10-02
N = 100
Fixation probability
10-04
10-06
= 2s (large, positive S,
large N)
N = 1000
= 1/(2N) when |s| < 1/(2N)
10-08
10-10
N = 10,000
10-12
10-14
-0.01
0
0.01
Selective advantage (s)
0.02
Real phylogenetic trees
The Rate of Evolution Depends on
Constraints
Human vs. Rodent Comparison
Highest substitution rates
pseudogenes
introns
3’ flanking (not transcribed
to mature mRNA)
4-fold degenerate sites
Intermediate substitution rates
5’ flanking (contains promoter)
3’, 5’ untranslated (transcribed
to mRNA)
2-fold degenerate sites
Lowest substitution rates
Nondegenerate sites
Selection of Species for DNA comparisons
Human versus
Chimpanzee
Mouse
Opossum
Pufferfish
Size (Gbp)
3.0
2.5
4.2
0.4
Time since
divergence
~5 MYA
~ 65 MYA
~150 MYA
~450 MYA
Sequence
conservation (in
coding regions)
>99%
~80%
~70-75%
~65%
Aids identification
of…
Recently
changed
sequences and
genomic
rearrangements
Both
Both
Primarily
coding and coding and
coding
non-coding non-coding sequences
sequences sequences
UCSC Genome
Browser
39
Comparative analysis of multi-species
sequences from targeted genomic regions
Nature, 2003
40
Comparative Genomics in the CFTR Region
Near CFTR
1.8 Mb of human Ch7, Sequenced for 12 ssp.
How does a region change over evolutionary time?
How much does it change?
What types of changes are more/less common?
Do some lineages have more of certain changes than
others?
How much comparative genomic data do we need???
Sequence Conservation
42
Looking backward from the human genome
How much is still there after 450my (Fugu)
43
Transposable Elements
Gone Wild!
Transposable Elements
Gone Wild!
45
Transposable Elements
Gone Wild!
46
Transposable Elements
Gone Wild!
47
Transposable Elements
Gone Wild!
BovB
CR1
48
Nucleotide Changes
Big insertions/deletions are
more common than
nucleotide changes!
In primates, large indels are
the principal mechanism
accounting for observed
sequence differences
49
Identifying Functionally Important Regions
How many comparative genomes do we need?
Can’t we just use the mouse?
Using 12 species,
561 Multi-Species
Conserved
Sequences
(MCSs) were
found
False Pos.
True Pos.
False Neg.
How can be
found using just
the Mouse
genome (rather
than all 12)
Multi-Species Conserved Sequences
950 of the 1,194 MCSs
are neither exonic nor
lie less than 1-kb
upstream of transcribed
sequence.
Meaning they are
otherwise hard to
predict
(Evolutionary Distance)
Strong argument for comparative genomics:
Need many species, and distant species – like cat, dog,
fish - to ID conserved possibly-functional regions in
humans!
51
Interpreting Evolutionary Changes
Requires a Model
…IGTLS…
…IGRLS...
In evolution:
what is the rate R(T R) at
which Ts become Rs?
e.g. 0.00005 / my
20 x 20
Substitution Matrix