Post on 19-Dec-2015
In memory of
John Maynard Smith
Phenotypic variability is omnipresent in nature
It takes all the running you can do to keep in the same place
If you want to get somewhere else, you must run at least twice as fast
Lewis Carroll, 1871
A B A B A B••••• •
intraspecific variability
environmentally induced adaptation
Lamarckian Paradigm
A B A B BA• • • • ••
Darwinian Paradigm
natural selection
natural selection
Darwinian evolution : variability, selection, transmission
time
Num
ber
of c
opie
s
Adaptives mutations : 0 1 2 3 4 5 6
Can be applied to any «amplifiable information» (Dawkins, 1976, « the selfish gene »)
Different types of MUTATIONS
Neutral
Lethal
Deleterious
Adaptives
10 -5
10 -4
10 -8
wildtype
mutS+
Mutator
mutS-
10 -3
10 -2
10 -6
Estimated total mutation rate for bacteria1 mutation / 300 genomes replicated
An invariant in evolution of DNA !? (Drake rule)
Mechanisms controlling the maintenance of genetic information
nucleotide pool
DNA repair
Fidelity of synthesis
post-replication control
Photoactivation Repair in E. coli
• Exposing UV treated cells to blue light results in a reversal of the thymine dimer formation
• Enzyme, photoactivation repair enzyme (PRE) absorbs a photon of light (from blue light) and is able to cleave the bond forming the thymine dimer.
• Once bond is cleaved, DNA is back to normal
Like other repair systemIt is conserved throughout evolution, conserved from bacteria (where first discovered)to man where they are involved in a variety of disease
Excision Repair
Xeroderma Pigmentosum & Nucleotide Excision Repair
• Xeroderma pigmentosum (XP)- is a rare genetic disorder that predisposes an individual to skin abnormalities
– Individuals lose the ability to undergo NER• UV radiation exposure leads to reactions from freckling and skin
ulceration to skin cancer
– Studies suggest many different genes may be involved in excision repair
– XP-variant is encoding a lesion by-pass DNA polymerase (SOS)
By-pass polymerasescan lead to error free or error prone (mutagenic) synthesis depending on the lesion
Oxidation of guanine lead to transversion
The Mismatch Repair System
ExoI, ExoVII, RecJ, UvrD, PolIII, SSB, Ligase
CH3
MutSMutL
CH3
MutH
Mismatch repair system• corrects replication errors • ensures global genomic stability • prevent tumour formation
Mismatch site
GATC-site
High polymorphism of mutation rates in commensal and pathogenic Escherichia coli natural isolates
7060 6550 5540 4530 3525201510501E-9
1E-8
1E-7
1E-6
1E-5
Frequency of mutations to Rif in mutator strains
Strain number
mutS-
mutS-
mutL-
mutL-
R
Commensals FranceCommensals MaliCommensals Croatia
UTIbacteremiapusneonatal meningitis
haemolytic-uremicsyndrome
I. Matic, M. Radman, F. Taddei, B. Picard, C. Doit, E. Bingen, E. Denamur and J. ElionScience (1997) vol. 277 p. 1833
mutS-
The frequencies of mutator among E. coli vary
with the associated pathologies
Denamur J. bacteriol. 2002
Number of virulence factors correlates with in vivo virulence
Picard Infect.Immun. 2001
only in non-mutator strains
Mutation rates are higher among strains with
intermediate virulence
Picard Infect.Immun. 2001
1E-05
1E-04
1E-03
1E-02
1E-01
1E+00
0 5000 10000 15000
Temps (générations)
Modélisation des mutateurs
Nature (1997) 387 700-702
Time (generations)
Mut
ator
fre
quen
cyModelling mutators frequencies during adaptation to a new environment
Tenaillon Genetics (1999)
Selecting for mutators is easier in larger population
Tenaillon Genetics (1999)
When mutation is rate limiting large population adapt much faster
log (population size)
Tenaillon Genetics (1999)
Mutator can speed up adaptation (even when rare)
log (population size)
Kiss meI ’m germ-
free
An in vivo model: an animal with a controled microbial flora
Giraud
Evolution of population size
mutS+
days
log
(pop
ulat
ion
size
)8,8
9,0
9,2
9,4
9,6
9,8
10,0
10,2
0 5 10 15 20
mutS+
mutS- mutS-
Mutator bacteria adapt faster to a new environment
Giraud Science 2001
Time (Days)
Mea
n lo
g(m
utat
or/w
ild t
ype)
0 1 2 3 4 5 6 7 8 9 10
-5
-4
-3
-2
-1
0
1
2
3
4
5
The initial population size influence the outcome of the competition
mutS-/mutS+
mutS-/ 50 mutS+
mutS-/ 50 000 mutS+
Giraud et al Science 2001
The population threshold for mutator victory
is 1/(mutation rate)
Mutator victory threshold is frequency independentLe Chat
The victory is stochastic with a constant expected gain
Le Chat
Once adaptation is achieved the mutator advantage is reduced
Mea
n l
og
(mu
tato
r/w
ild
typ
e)
-1
-0.5
0
0.5
1
1.5
2
2.5
3
3.5
0 1 2 3 4 5 6 7 8 9 10Time (Days)
Naive
adapted
Giraud et al Science 2001
WT+Mut MutWT
Mutators & migration in vivo
-1
0
1
2
3
0 2 4 6 8 10Days
Log
(mut
S- / m
utS+
)
-1
0
1
2
3
0 2 4 6 8 10Days
Log
(mut
S- / m
utS+
)The benefit of the mutator is reduced in presence of migration
Controlling migration timing in vitro
WT Mut
0 12 24
hours
migration
24 h
migration
24 h
media: LB + Spc
Mut : mutS-
15 18 21
V VV V
Le Chat
55,5
66,5
77,5
88,5
99,510
9 12 15 18 21 24
log
(C
FU
)
Mutator population adapt faster
mutator
nonmutator
The benefit of the mutator disappears if adaptation is over before migration
"migration"
-0,5
0
0,5
1
1,5
2
2,5
3
9 12 15 18 21 24lo
g (
mu
tato
r/W
T)
Mutator bacteria suffer from genetic amnesia
mutS- ancestormutS+ ancestor
Days post inoculum
Mean % of auxotrophs
100 150 200 250 3000
510
15
202530
ndnd
Emergingmutator
non mutator
Giraud et al Science 2001
23456789
1011
0 5fos spc
4 mice
10 15
Impact of antibiotic treatments on mutation rates
Log
(po
pula
tion
size
)
20fos spc fos spc
23456789
1011
0 5 10 15 20
1 mouse
2023456789
1011
0 5 10 15
1 mouse
Rpopulation Rif
fosspc
time
Day 0 : inoculation
Measures of population sizes
streptomycinNalidixic acid
23456789
1011
0 5 10 15 20
1 mouse
fos spc20
23456789
1011
0 5 10 15
1 mouse
fos spc
str + nal
Impact of mutation rates on bacterial survival to antibiotic treatments
2
3
4
5
6
7
8
9
1011
0 5 10
Log
( p
opul
atio
n si
ze)
non mutator
mutator
How many antibiotics should be used against mutator bacteria ?
Percentage of treatment failure
Number of antibiotics administered simultaneously
Ancestral genotype1 2 3
Antimutator (mutS+) 100 0 (+17*) n.d.
Mutator (mutS-) n.d. 70 0
*emerging mutator (2 mutS-)
Giraud AAC (2002)
Denamur J. bacteriol. 2002
Mutator bacteria are more likely to become antibiotic resistant
Non mutator (A) and mutator (B) phenotypes on antibiograms
Denamur et al J. bacteriol 2002
Mutators are abundant and more antibiotic resistant among P. aeruginosa infecting Cystic Fibrosis patients
Oliver Science (2000)
Mutator (CF)
Non-mutator (CF)
Non-CF
Resistance accumulate 3 times faster in patients colonised by mutators
MutatorNon mutator
delay (days)
Pro
babi
lity
of
incr
ease
d re
sist
ance
Moumile
Mutator can speed up cellular evolution
time
Cel
l num
ber
time
Cel
l num
ber Mutator sub-population
Adaptives mutations
0 1 2 3 4 5 6
The bacterial Red Queen
Why change ?Population geneticsGodelle Gouyon Brown Maynard-Smith
Change where ?Microbial ecology Fons
Who changes ?Molecular epidemiologyBinguen Denamur Picard Brisabois Berche
A network approach of bacterial variability
GiraudLechatBambou
B. ToupanceO. TenaillonJ-B André
Duriez
Change what?Bio-informaticsRocha
Who has changed ?Molecular PhylogenyLecointre Darlu
How to change ? Molecular biology Matic Radman Vulic Dionisio BjedovBregeon Leroy Hayakawa Sekiguchi Dukan
Change when ?transcriptome analysis Knudsen Cerf
Phenotypic variabilityLife History Stewart Madden Lindner Paul Gabriel Fontaine Depaepe Bredèche Mosser
Moumile
Diard
www.necker.fr/tamara/
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Hyper-recombination phenotypes of
mismatch repair mutants
Denamur Cell (2000)
BB
A
A
Holliday junction
Splice
Patch
+
+
Homologous Recombination
• exchange of DNA 1strands to form heteroduplex DNA
• cleavage of Holliday junction at A or B
• religation to recombinant products
A: splice products B: patch products
The barrier to recombination is DNA sequence divergence
Vulic PNAS (1997)
Holliday junction
Splice
Patch
+
+
Homeologous Recombination
• divergent sequences do not recombine efficiently
• mismatch repair prevents formation of recombination intermediates
• in mismatch repair deficient background homeologous recombination proceeds to generate mosaic genes and genomes
mismatch +mismatch -
Effect of Mismatch Repair System on InterspeciesRecombination
Inhibition of Mismatch Repair System
• increases homeologous recombination to the level of homologous recombination and thus allows interspecies recombination
• allows broadest genetic variability in vivo
• broad area of applications• generation of novel low molecular weight entities• generation of modified and optimised macromolecules• generation of (micro)organisms with desired properties
Homeologous Recombination In Vivo
Mosaic Genes Mosaic Genomes
Mosaic Proteins Mosaic Pathways
A´
D´
B´
C´
A
D
B
CC´´
D´´
Novel Products
The bacterial Red Queen
Why change ?Population geneticsGodelle Gouyon Brown Maynard-Smith
Change where ?Microbial ecology Fons
Who changes ?Molecular epidemiologyBinguen Denamur Picard Brisabois Berche
A network approach of bacterial variability
GiraudLechatBambou
B. ToupanceO. TenaillonJ-B André
Duriez
Change what?Bio-informaticsRocha
Who has changed ?Molecular PhylogenyLecointre Darlu
How to change ? Molecular biology Matic Radman Vulic Dionisio BjedovBregeon Leroy Hayakawa Sekiguchi Dukan
Change when ?transcriptome analysis Knudsen Cerf
Phenotypic variabilityLife History Stewart Madden Lindner Paul Gabriel Fontaine Depaepe Bredèche Mosser
Moumile
Diard
www.necker.fr/tamara/
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Most genes in E. coli genome have a common history
Denamur Cell (2000)
Phylogenetic trees of mismatch repair genes show horizontal transfers
Denamur Cell (2000)
Inferred horizontal transfers in mutU gene
Denamur Cell (2000)
Inferred horizontal transfers in mutS gene
Denamur Cell (2000)
Horizontal transfers are more abundant in mismatch repair genes
Denamur Cell (2000)
Hyper-recombination phenotypes of
mismatch repair mutants
Denamur Cell (2000)
Hyper-rec phenotypes of mutator genes correlate with their sequence mosaicisms
Denamur Cell (2000)
Mutator bacteria suffer from genetic amnesia
mutS- ancestormutS+ ancestor
Days post inoculum
Mean % of auxotrophs
100 150 200 250 3000
510
15
202530
ndnd
Emergingmutator
non mutator
Giraud et al Science 2001
Role of mutator in adaptive evolution
The bacterial Red Queen
Why change ?Population geneticsGodelle Gouyon Brown Maynard-Smith
Change where ?Microbial ecology Fons
Who changes ?Molecular epidemiologyBinguen Denamur Picard Brisabois Berche
A network approach of bacterial variability
GiraudLechatBambou
B. ToupanceO. TenaillonJ-B André
Duriez
Change what?Bio-informaticsRocha
Who has changed ?Molecular PhylogenyLecointre Darlu
How to change ? Molecular biology Matic Radman Vulic Dionisio BjedovBregeon Leroy Hayakawa Sekiguchi Dukan
Change when ?transcriptome analysis Knudsen Cerf
Phenotypic variabilityLife History Stewart Madden Lindner Paul Gabriel Fontaine Depaepe Bredèche Mosser
Moumile
Diard
www.necker.fr/tamara/
QuickTime™ et un décompresseurPhoto - JPEG sont requis pour visualiser
cette image.
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cette image.
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How to adapt to predictable
impredictability ?
start stop
ORF
duplication
deletionconversion
Recombination between close repeats
Recombination between SSR
st art stop
ORF
XXXXXX XXXXXXXX
delet ion
XXXX
duplicat ion
Localized mutators
Rocha Nucleic Acid Research (2002)
x y
x x x
x x y
Close direct repeats
gene500 bp 500 bp
1 2
1 2
1 2
L < 1000 ntObserved
Observed in 1000 random sequences
of equal length and 3-tuple composition
ObservedExpected = 1.9Over-represented classes:
• Recombination, repair• Transcription, RNA degradation
• Translation• Transport proteins
Close direct repeats.
5
10
0 10 20 30Number of close repeats in gene
0
gene500 bp 500 bp
1 2
1 2
1 2
L < 1000 ntStress response
genes
All E. coli K12genes
Rocha NAR (2002)
aab
bcccc
dddd e
eff
gg h
hh
hhh
iii
i
jjkk ll
dnaA
position (kb)
a ab b b
b
c c c
cd
d
e
eg
g
h hi
ij
j
k k
l l
m
mn n
o
op p
q
qr rf
f
betB
b
b
c
c c c
c
c
c d de ef
f f
g g
h
h hm m
n
n oop pl
l
k kj
ji
i a a
mutS
a
abb
cc c
d dd d d
d
d de e
csgA
a
a
b
b
c c
d d e ef
f g gh
h
i
i
i
j j
k
k
k
n n n n n q q
p
p
o
o m m l
lmutL
a
a
a
a
a a
a
a
f
f
g g
h
he e
ee
ee
e e
e
e
e
e
e e
e
ed
d
d d dc c b
b baceF
a
a b b b bc
c
c c
c
c
c
c c
f
f g
gm m
p
p p
q
qr rs
su u
v v t t
o oo
n
n
n n
n
ll l lkj j
i
ih
h
e
ed dsbcC
a a
b
b
bc c
c
e e
e
f
f
i iik kl ln no op p
lamB
a a
bc cd dfg h il mnj e
b bcd d df gh i l mo o k kje
cyoE
a
ab
b bc c c c
c
d
d
f fj ji ih hg g
e e
cyoC
a
ab b bc c d d
e
ef fg g
g
i i
h
h
sodB
0
0
0
0
00
0 0
0 0
1
2 4
3
position (kb)0 3
gene
occurrence of the repeat
b repeat label
21 21
21
21
21
21
21 31
1
1
Rocha NAR (2002)