Metabolic and evolutionary patterns in the extremely acidophilic archaeon Ferroplasma acidiphilum YT
| Autor: | Alexander Goesmann, Oleg N. Reva, Michail M. Yakimov, Sofia Lemak, Alexei I. Slesarev, Peter N. Golyshin, Hai Tran, Violetta LaCono, David Rojo, Francesco Smedile, Olga V. Golyshina, Alexander F. Yakunin, Manuel Ferrer, Coral Barbas, Taras Y. Nechitaylo |
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| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
Genome evolution Mutation rate Science Biology Ferroplasma medicine.disease_cause DNA Mismatch Repair Genome Article Evolution Molecular 03 medical and health sciences Genome Archaeal medicine Clustered Regularly Interspaced Short Palindromic Repeats Amino Acids Gene Recombination Genetic 2. Zero hunger Genetics Mutation Multidisciplinary Ecology Ferroplasma acidiphilum Genomics Carbon Dioxide biology.organism_classification Archaea Biological Evolution Carbon 030104 developmental biology Gene Expression Regulation Medicine Energy Metabolism Metabolic Networks and Pathways |
| Zdroj: | Scientific Reports Scientific Reports, Vol 7, Iss 1, Pp 1-12 (2017) |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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