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.
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.
Moreira
David
D
UMR CNRS 8079, Ecologie, Systématique et Evolution, Université Paris-Sud, bâtiment 360, 91405 Orsay Cedex, France.
Rodríguez-Valera
Francisco
F
López-García
Purificación
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D001426:Bacterial Proteins / Q000235:genetics*; D001483:Base Sequence; D001499:Bayes Theorem; D017931:DNA Primers; D004734:Energy Metabolism / Q000235:genetics; D019605:Euryarchaeota / Q000235:genetics*; D040461:Gene Components; D016680:Genome, Bacterial; D016013:Likelihood Functions; D008957:Models, Genetic; D008969:Molecular Sequence Data; D009792:Oceans and Seas; D009876:Operon / Q000235:genetics; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics; D017422:Sequence Analysis, DNA; D000198:Spectinomycin
D001426:Bacterial Proteins; D017931:DNA Primers; D012336:RNA, Ribosomal, 16S; D000198:Spectinomycin