title: Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group.
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.
authors.affiliation: Subsurface Geobiology & Advanced Research Project, Institute of Biogeosciences, Japan Agency for Marine-Earth Science & Technology, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan. takuron@jamstec.go.jp
authors.forename: Takuro
authors.initials: T
authors.lastname: Nunoura
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Takaki
authors.forename: Jungo
authors.initials: J
authors.lastname: Kakuta
authors.forename: Shinro
authors.initials: S
authors.lastname: Nishi
authors.forename: Junichi
authors.initials: J
authors.lastname: Sugahara
authors.forename: Hiromi
authors.initials: H
authors.lastname: Kazama
authors.forename: Gab-Joo
authors.initials: GJ
authors.lastname: Chee
authors.forename: Masahira
authors.initials: M
authors.lastname: Hattori
authors.forename: Akio
authors.initials: A
authors.lastname: Kanai
authors.forename: Haruyuki
authors.initials: H
authors.lastname: Atomi
authors.forename: Ken
authors.initials: K
authors.lastname: Takai
authors.forename: Hideto
authors.initials: H
authors.lastname: Takami
mesh_terms: D000595:Amino Acid Sequence; D001105:Archaea / Q000145:classification / Q000235:genetics / Q000378:metabolism; D019843:Archaeal Proteins / Q000737:chemistry / Q000235:genetics*; D001483:Base Sequence; D002453:Cell Cycle / Q000235:genetics; D004260:DNA Repair; D004261:DNA Replication; D004734:Energy Metabolism / Q000235:genetics; D019143:Evolution, Molecular; D019766:Genes, Archaeal; D020745:Genome, Archaeal; D015698:Genomic Library; D006360:Heat-Shock Proteins / Q000235:genetics; D054892:Metagenome; D008969:Molecular Sequence Data; D010802:Phylogeny; D014176:Protein Biosynthesis; D016415:Sequence Alignment; D014158:Transcription, Genetic; D014452:Ubiquitins / Q000737:chemistry / Q000235:genetics*
chemical_list: D019843:Archaeal Proteins; D006360:Heat-Shock Proteins; D014452:Ubiquitins