Evolutionary Biology Group

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Genomes and Evolution
Evolutionary Biology Group Isabel Gordo
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Evolutionary change
-Rate of mutation -Strenght of natural
selection -level of interaction between mutations
- epistasis
Understanding the evolution of any biological
system depends upon understanding each of these
mechanisms
Estimates of these parameters in bacteria will
have a profound impact on our understanding of
their biology, their diversity, their rate of
speciation and in our health. Experimental
Evolution with bacteria allows us to directly
measure these parameters and to test theoretical
predictions about the genetic basis of adaptive
evolution.
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Mutation, selection and epistasisin Escherichia
coli
Is there a law governing its adaptation?
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R.A. Fisher and a microscope
A random mutation of large effect has much higher
change of being deleterious than of being
beneficial
Most beneficial mutations have small effects on
fitness
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Study of adaptation in E. coli while it is
occurring
Genetically modify the bacteria to measure
adaptive mutations as they get incorporated in
the population
Imhof M, Schlotterer C. PNAS 2001
One adaptive event- selective sweep
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The rate of mutation to beneficial alleles can be
as high as 2x10-51 in 150 new mutations can be
advantageous
Ua2x10-5 per genome per generation E(Sa)0.01
Perfeito et al. Science 2007
Compatible with Fisher adaptive mutations of
large effect are rarer
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Epistasis and evolution of antibiotic resistance

• Mutations confering antibiotic resistance have a
  benefit when the drug exists in the environments
• Mutations confering antibiotic resistance have a
  cost in drug free environments

If a pathogenic strain is resistant to antibiotic
X, which antibiotic should be administered as a
second treatment?
Best combination is that which leads to the
higher cost.
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What is the cost of multiple antibiotic
resistance?
X
Cost of mutation c1
Resistant to antibiotic 1
Cost of mutation c2
X
Resistant to antibiotic 2
X
X
Cost of mutation 1 2 ?
Resistant to both antibiotics
If c12 c1 c2 No epistasis, no interaction
e0 If c12 gt c1 c2 Negative epistasis, high
cost elt0 If c12 lt c1 c2 Positive epistasis,
low cost egt0
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1) Select resistant clones
rpsL K43N
X

• Antibiotics used
• nalidixic acid, which inhibits DNA replication by
  binding to DNA gyrase
• rifampin, binds to the b-subunit of RNA
  polymerase thereby inhibiting transcription
• (iii) streptomycin, binds to the ribosome and
  inhibits elongation of protein synthesis

2) Make all possible combinations of double
resistant clones
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Major finding 1
combinations with positive epistasis gt with
negative epistasis
The cost of double resistance is lower than
expected
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Major finding 2
Resistance mutations to a new antibiotic can
compensate the cost of resistance to another
antibiotic
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"What is true for E. coli is true for the
elephant," Jacques Monod
M. tuberculosis
E. coli
Low cost for resistance mutations X and Y
High frequency of multiple resistance involving X
and Y
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Conclusions

• We estimated that 1 in 150 mutations can be
  adaptive
• This is the highest estimate ever obtained in a
  bacteria
• The mean effect of each new beneficial mutations
  is about 1.
• The data supports the Fisherian hypothesis that
  most beneficial mutations have small effects and
  those that will fix follow a gamma distribution

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Conclusions

• We estimated that 1 in 150 mutations can be
  adaptive
• This is the highest estimate ever obtained in a
  bacteria
• The mean effect of each new beneficial mutations
  is about 1.
• The data supports the Fisherian hypothesis that
  most beneficial mutations have small effects and
  those that will fix follow a gamma distribution
• Double antibiotic resistance is less costly than
  we could a priori predict
• Very difficult to eliminate resistant bacteria
• Some resistance mutations which are deleterious
  when in a wild-type background are beneficial
  (compensatory) when in a genetic background that
  contains another resistance gt Sign epistasis

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Conclusions
Together these results are the worst nightmare
for the host and the best dream for the microbe.
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Thanks to

• Lisete Fernandes (IGC)
• Ana Margarida Sousa(IGC)
• Francisco Dionisio (FCUL)
• Karina Xavier(IGC/ITQB)
• Miguel Godinho Ferreira(IGC)

Lilia Perfeito Sandra Trindade
Thank you all!!!
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Evolutionary questions on mutation

• Is there an optimal mutation rate?
• What is the optimal mutation rate?

R.A. Fisher 1930 The genetical theory of natural
selection optimal U must have an intermediate
value
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Drakes Rule
Genomic mutation rate in DNA microbes is
constant
Drakes U0.003 (Drake et al. 1998)
Review by Sniegowski et al (2000)- PinkRNA
viruses (rv, rhinovirus pv, poliovirus vsv,
vesicular stomatitis virus mv, measles
virus). Red DNA phages M13, T2, T4, and ?. E.
coli (Ec) Saccharomyces cerevisiae (Sc)
Neurospora crassa (Nc) Ce C. elegans Dm
Drosophila melanogaster Mm, Mus musculus Hs,
Homo sapiens