Metabolic and evolutionary patterns in the extremely acidophilic archaeon Ferroplasma acidiphilum YT

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  • Olga Golyshina
  • Tran Hai
  • Olga N. Reva
    University of Pretoria
  • Sofia Lemak
    University of Toronto, Canada
  • Alexander F. Yakunin
    University of Toronto, Canada
  • Alexander Goesmann
    Bielefeld University
  • Taras Y. Nechitaylo
    Max Planck Institute for Chemical Ecology, Jena.
  • Violetta LaCono
    Institute for Coastal Marine Environment
  • Francesco Smedile
    Institute for Coastal Marine Environment
  • Alexei Slesarev
    Fidelity Systems, Zylacta Corporation, USA
  • David Rojo
    Universidad CEU San Pablo, Madrid
  • Coral Barbas
    Universidad CEU San Pablo, Madrid
  • Manuael Ferrer
    CSIC, Institute of Catalysis, Madrid
  • Michail M. Yakimov
    Institute for Coastal Marine Environment
  • Peter Golyshin
Ferroplasmaceae represent ubiquitous iron-oxidising extreme acidophiles with a number of unique physiological traits. In a genome-based study of Ferroplasma acidiphilum YT, the only species of the genus Ferroplasma with a validly published name, we assessed its central metabolism and genome stability during a long-term cultivation experiment. Consistently with physiology, the genome analysis points to F. acidiphilum YT having an obligate peptidolytic oligotrophic lifestyle alongside with anaplerotic carbon assimilation. This narrow trophic specialisation abridges the sugar uptake, although all genes for glycolysis and gluconeogenesis, including bifunctional unidirectional fructose 1,6-bisphosphate aldolase/phosphatase, have been identified. Pyruvate and 2-oxoglutarate dehydrogenases are substituted by ‘ancient’ CoA-dependent pyruvate and alpha-ketoglutarate ferredoxin oxidoreductases. In the lab culture, after ~550 generations, the strain exhibited the mutation rate of ≥1.3 × 10−8 single nucleotide substitutions per site per generation, which is among the highest values recorded for unicellular organisms. All but one base substitutions were G:C to A:T, their distribution between coding and non-coding regions and synonymous-to-non-synonymous mutation ratios suggest the neutral drift being a prevalent mode in genome evolution in the lab culture. Mutations in nature seem to occur with lower frequencies, as suggested by a remarkable genomic conservation in F. acidiphilum YT variants from geographically distant populations.
Original languageEnglish
Article number3682
JournalScientific Reports
Early online date16 Jun 2017
Publication statusPublished - 16 Jun 2017

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