极端嗜酸古菌的单菌基因组分析套路
  • 铁质体科(Ferroplasmaceae)是一种普遍存在的铁氧化极端嗜酸菌,具有许多独特的生理特性;
  • 基因组分析表明F. acidiphilum YT具有专性的蛋白分解营养型的生活方式和具有回补型碳同化途径;
  • 基因组中检测出糖酵解和糖异生途径的所有基因;
  • 在实验室培养经过550代后,该菌株每代的单核苷酸取代率是单细胞生物中已有记录中的最高值;
  • 地理上相隔遥远的F. acidiphilum群体中显著的基因组保守性说明自然界中的突变似乎以较低的频率发生。
主编推荐语
刘永鑫-中科院-宏基因组
Ferroplasma是极端酸性环境中极难分离培养的古菌,该研究首次获得Ferroplasma acidiphilum的全基因组完成图,获得了其代谢和进化的基本情况,同时为深入研究他们的进化地位、自然生态中的角色和功能提供了基础。
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Scientific Reports [IF:3.998]

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

极端嗜酸古菌嗜酸性铁质体的代谢和进化模式

10.1038/s41598-017-03904-5

2017-06-16, Article

Abstract & Authors:展开

Abstract:收起
erroplasmaceae 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.

First Authors:
Olga V Golyshina

Correspondence Authors:
Olga V Golyshina

All Authors:
Olga V Golyshina,Hai Tran,Oleg N Reva,Sofia Lemak,Alexander F Yakunin,Alexander Goesmann,Taras Y Nechitaylo,Violetta LaCono,Francesco Smedile,Alexei Slesarev,David Rojo,Coral Barbas,Manuel Ferrer,Michail M Yakimov,Peter N Golyshin

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