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Evolutionary Conservation of Bacterial Essential Metabolic Genes across All Bacterial Culture Media

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  • Oren Ish-Am
  • David M Kristensen
  • Eytan Ruppin

Abstract

One of the basic postulates of molecular evolution is that functionally important genes should evolve slower than genes of lesser significance. Essential genes, whose knockout leads to a lethal phenotype are considered of high functional importance, yet whether they are truly more conserved than nonessential genes has been the topic of much debate, fuelled by a host of contradictory findings. Here we conduct the first large-scale study utilizing genome-scale metabolic modeling and spanning many bacterial species, which aims to answer this question. Using the novel Media Variation Analysis, we examine the range of conservation of essential vs. nonessential metabolic genes in a given species across all possible media. We are thus able to obtain for the first time, exact upper and lower bounds on the levels of differential conservation of essential genes for each of the species studied. The results show that bacteria do exhibit an overall tendency for differential conservation of their essential genes vs. their non-essential ones, yet this tendency is highly variable across species. We show that the model bacterium E. coli K12 may or may not exhibit differential conservation of essential genes depending on its growth medium, shedding light on previous experimental studies showing opposite trends.

Suggested Citation

  • Oren Ish-Am & David M Kristensen & Eytan Ruppin, 2015. "Evolutionary Conservation of Bacterial Essential Metabolic Genes across All Bacterial Culture Media," PLOS ONE, Public Library of Science, vol. 10(4), pages 1-15, April.
    • Handle: RePEc:plo:pone00:0123785
    DOI: 10.1371/journal.pone.0123785
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    References listed on IDEAS

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    1. Csaba Pál & Balázs Papp & Laurence D. Hurst, 2003. "Rate of evolution and gene dispensability," Nature, Nature, vol. 421(6922), pages 496-497, January.
    2. Aaron E. Hirsh & Hunter B. Fraser, 2001. "Protein dispensability and rate of evolution," Nature, Nature, vol. 411(6841), pages 1046-1049, June.
    3. Aaron E. Hirsh & Hunter B. Fraser, 2003. "Rate of evolution and gene dispensability," Nature, Nature, vol. 421(6922), pages 497-498, January.
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