Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group

Takuro Nunoura, Yoshihiro Takaki, Jungo Kakuta, Shinro Nishi, Junichi Sugahara, Hiromi Kazama, Gab Joo Chee, Masahira Hattori, Akio Kanai, Haruyuki Atomi, Ken Takai, Hideto Takami

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186 Citations (Scopus)

Abstract

The domain Archaea has historically been divided into two phyla, the Crenarchaeota and Euryarchaeota. Although regarded as members of the Crenarchaeota based on small subunit rRNA phylogeny, environmental genomics and efforts for cultivation have recently revealed two novel phyla/divisions in the Archaea; the 'Thaumarchaeota' and 'Korarchaeota'. Here, we show the genome sequence of Candidatus 'Caldiarchaeum subterraneum' that represents an uncultivated crenarchaeotic group. A composite genome was reconstructed from a metagenomic library previously prepared from a microbial mat at a geothermal water stream of a sub-surface gold mine. The genome was found to be clearly distinct from those of the known phyla/divisions, Crenarchaeota (hyperthermophiles), Euryarchaeota, Thaumarchaeota and Korarchaeota. The unique traits suggest that this crenarchaeotic group can be considered as a novel archaeal phylum/division. Moreover, C. subterraneum harbors an ubiquitin-like protein modifier system consisting of Ub, E1, E2 and small Zn RING finger family protein with structural motifs specific to eukaryotic system proteins, a system clearly distinct from the prokaryote-type system recently identified in Haloferax and Mycobacterium. The presence of such a eukaryote-type system is unprecedented in prokaryotes, and indicates that a prototype of the eukaryotic protein modifier system is present in the Archaea.

Original languageEnglish
Pages (from-to)3204-3223
Number of pages20
JournalNucleic Acids Research
Volume39
Issue number8
DOIs
Publication statusPublished - 2011 Apr
Externally publishedYes

ASJC Scopus subject areas

  • Genetics

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    Nunoura, T., Takaki, Y., Kakuta, J., Nishi, S., Sugahara, J., Kazama, H., Chee, G. J., Hattori, M., Kanai, A., Atomi, H., Takai, K., & Takami, H. (2011). Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group. Nucleic Acids Research, 39(8), 3204-3223. https://doi.org/10.1093/nar/gkq1228