Transcript E. coli Genome Evolution and Adaptation

Genome evolution and adaptation in a long-term
experiment with Escherichia coli [1]
Richard Wolfe
Introduction




Adaptation – a change that improves an organisms
chances of survival and reproduction
Mutations are not necessarily beneficial.
In order to examine the tempo and mode of genomic
evolution, 40,000 generations of E.coli were sequenced.
The genomes were sequenced at 2K, 5K, 10K, 15K, 20K
and 40K generations.

These genomes were compared to the ancestral stain.

Almost 20 year long experiment.

Glucose was limiting nutrient.

12 populations
Introduction

Deletion – nucleotide removed

Insertion – nucleotide added

IS insertion – insertion sequence – entire sequence added

Inversion – section removed, inverted, reinstalled

45 mutations in 20K generation


Include 29 single-nucleotide polymorphisms SNPs
inserted
Include 16 deletions, insertions and other polymorphisms
DIPs
Mutations Found
Rates of Genomic and Fitness Improvement
Discussion





Genomic evolution is near-linear.
Normally this would suggest neutral evolution, mutations
do not matter.
Fitness is not linear and the rate of improvement slows
down over time.
Indicates that the rate beneficial mutations are occuring is
declining and/or their their average benefit is becoming
smaller.
These effects should cause the rate of genomic evolution
to decelerate but, it remains the same.
Discussion




Hypothesis: only a small fraction of all substitutions are
beneficial and most are neutral. The beneficial
substitutions occur in early generations and adapt to the
conditions of the experiment. The neutral mutations occur
later and the rate of fitness improvement slows down.
Evidence to reject hypothesis:
1. You would expect to find mutations that did not change
the protein sequence but, all 26 point mutations found in
coding regions (22 in 20K) changed the protein sequence.
2. You would not expect to see mutations in the same
genes in the other 11 populations if due to random drift but
if by selection then same genes would be mutated
because they evolved in same environments.
Discussion

3 cases where all 11 populations have substitutions in same gene

9 genes have mutations in other lines

Only 2 cases where no mutation has occured
Discussion


3. You would expect many mutations would not become
fixed but, almost all mutations that occur early are present
in the rest of the generations.
4. Strains with neutral mutations would have no fitness
advantage but, isogenic strains with ancestral and derived
alleles show a significant advantage.
40K Genome Analysis

After 26K generations a greatly elevated rate of genomic
evolution occured.

40K genome contained 627 SNP and 26 DIP mutations

40K genome 1.2% smaller than ancestor.

Unlike the mutations before 20K, only a small number of
these later mutations are beneficial
References
1. Barrick JE, Yu DS, Yoon SH, Jeong H, Oh TK, Schneider D,
Lenski RE, Kim JF; Genome evolution and adaptation in a
long-term experiment with Escherichia coli. Nature. October
2009, 461:1243-1247.