Life History Traits and Genome Structure

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Life History Traits and Genome Structure

• Aerobiosis and GC Content in Bacteria

J.R. Lobry Université Claude Bernard - Lyon
I CNRS UMR 5558 INRIA Helix FRANCE
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(No Transcript)
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Aerobic versus Anaerobic

• You need the presence of O2 to live, you are
  aerobic (obligate)
• You need the absence of O2 to live, you are
  anaerobic (obligate)
• ...snip...

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Anaerobic and Aerobic Species
Only Anaerobic Species
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Aerobic gtgt Anaerobic

• In aerobic conditions (with O2) the oxydation of
  one molecule of glucose (respiration) yields 38
  ATP (metabolic currency unit). Short generation
  times.
• In anaerobic conditions (without O2) the
  fermentation of one molecule of glucose yields 2
  ATP (metabolic currency unit). Long generation
  times.

The generation time is a life history trait
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Life History Traits and Genome Structure

• Aerobiosis and GC Content in Bacteria

J.R. Lobry Université Claude Bernard - Lyon
I CNRS UMR 5558 INRIA Helix FRANCE
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Bacteria in the Universal Tree of Life
Saccharomyces
Oryza
EUCARYA
Prorocentrum
Drosophila
Tetrahymena
Crithidia
ARCHAEA
Homo
Physarum
Halococcus
Halobacterium
Methanococcus
?
Methanobacterium
Desulfurococcus
Thermoproteus
EUBACTERIA
Thermus
Streptomyces
 BACTERIA 
Anacystis
Escherichia
Bacillus
Pseudomonas
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Bacteria and Eucarya
Only Bacteria
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Bacterial GenomesCircular dsDNA
Here GC 50
The GC content is a genome structure
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Life History Traits and Genome Structure

• Aerobiosis and GC Content in Bacteria

J.R. Lobry Université Claude Bernard - Lyon
I CNRS UMR 5558 INRIA Helix FRANCE
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Aerobiosis and GC Content in Bacteria
Aerobic
Anaerobic
Naya et al. (2002) J. Mol. Evol., 55260
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Aerobiosis and GC Content in Bacteria
Aerobic
Anaerobic
Why?
Naya et al. (2002) J. Mol. Evol., 55260
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Metabolic cost of amino-acids in Aerobiosis
38.3 ATP
11.7 ATP
52.0 ATP
11.7 ATP
27.3 ATP
14.7 ATP
15.3 ATP
27.3 ATP
Akashi Gojobori (2002) PNAS, 993695
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From amino-acid cost to Protein cost
Protein cost in ATP
Protein concentration in cells
Akashi Gojobori (2002) PNAS, 993695
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So what?
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The growth of genomic data
But available fossil DNA is lt 0.00013 109 years...
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All data are here
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Dataset

• 300 bacterial species
• 1,000,000 proteins
• 100,000,000 amino-acids

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Akashi (2002)
Naya (2002)
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Interpretation
Aerobic bacteria have a higher genomic GC
content than anerobic bacteria because this
induces an average protein composition which is
less expensive in aerobic conditions
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Life History Traits and Genome Structure

• Aerobiosis and GC Content in Bacteria

J.R. Lobry Université Claude Bernard - Lyon
I CNRS UMR 5558 INRIA Helix FRANCE