Analysis of a genome fragment of a deep-sea uncultivated Group II euryarchaeote containing 16S rDNA, a spectinomycin-like operon and several energy metabolism genes

Environ Microbiol. 2004 Sep;6(9):959-69. doi: 10.1111/j.1462-2920.2004.00644.x.


We have sequenced and analysed a 39.5 kbp genome fragment of a marine Group II euryarchaeote identified in a metagenomic library of 500 m deep plankton at the Antarctic Polar Front. The clone contains a 16S rRNA gene that is separated from the 23S rRNA gene in the genome. This appears to be a trait shared by Thermoplasmatales and Group II euryarchaeota. This genome fragment exhibits a compact organization, including a few overlapping genes in the canonical spectinomycin-like (spc) operon for ribosomal proteins that is immediately upstream the 16S rDNA. Most open reading frames (ORFs) encoded proteins involved in housekeeping processes and, as expected, exhibited a phylogenetic distribution congruent with that of the 16S rRNA. A considerable number of proteins with predicted transmembrane helices was identified. Among those, two proteins encoded by genes likely forming an operon appear to be part of a membrane terminal electron transport chain. One of these proteins has an unusual domain arrangement including ferredoxin, flavodoxin and one succinate dehydrogenase/fumarate reductase subunit. These proteins probably constitute a new succinate dehydrogenase-like oxidoreductase involved in what could be a novel pathway for energy metabolism in Group II euryarchaeota.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / genetics*
  • Base Sequence
  • Bayes Theorem
  • DNA Primers
  • Energy Metabolism / genetics
  • Euryarchaeota / genetics*
  • Gene Components
  • Genome, Bacterial*
  • Likelihood Functions
  • Models, Genetic
  • Molecular Sequence Data
  • Oceans and Seas
  • Operon / genetics
  • Phylogeny*
  • RNA, Ribosomal, 16S / genetics
  • Repetitive Sequences, Nucleic Acid / genetics
  • Sequence Analysis, DNA
  • Spectinomycin


  • Bacterial Proteins
  • DNA Primers
  • RNA, Ribosomal, 16S
  • Spectinomycin

Associated data

  • GENBANK/AY534910