title: Three binding sites for stalk protein dimers are generally present in ribosomes from archaeal organism.
abstract: Ribosomes have a characteristic protuberance termed the stalk, which is indispensable for ribosomal function. The ribosomal stalk has long been believed to be a pentameric protein complex composed of two sets of protein dimers, L12-L12, bound to a single anchor protein, although ribosomes carrying three L12 dimers were recently discovered in a few thermophilic bacteria. Here we have characterized the stalk complex from Pyrococcus horikoshii, a thermophilic species of Archaea. This complex is known to be composed of proteins homologous to eukaryotic counterparts rather than bacterial ones. In truncation experiments of the C-terminal regions of the anchor protein Ph-P0, we surprisingly observed three Ph-L12 dimers bound to the C-terminal half of Ph-P0, and the binding site for the third dimer was unique to the archaeal homologs. The stoichiometry of the heptameric complex Ph-P0(Ph-L12)(2)(Ph-L12)(2)(Ph-L12)(2) was confirmed by mass spectrometry of the intact complex. In functional tests, ribosomes carrying a single Ph-L12 dimer had significant activity, but the addition of the second and third dimers increased the activity. A bioinformatics analysis revealed the evidence that ribosomes from all archaeal and also from many bacterial organisms may contain a heptameric complex at the stalk, whereas eukaryotic ribosomes seem to contain exclusively a pentameric stalk complex, thus modifying our view of the stalk structure significantly.
authors.affiliation: Department of Biology, Faculty of Science, Niigata University, Ikarashi 2-8050, Niigata, Japan.
authors.forename: Yasushi
authors.initials: Y
authors.lastname: Maki
authors.forename: Tetsuo
authors.initials: T
authors.lastname: Hashimoto
authors.forename: Min
authors.initials: M
authors.lastname: Zhou
authors.forename: Takao
authors.initials: T
authors.lastname: Naganuma
authors.forename: Jun
authors.initials: J
authors.lastname: Ohta
authors.forename: Takaomi
authors.initials: T
authors.lastname: Nomura
authors.forename: Carol V
authors.initials: CV
authors.lastname: Robinson
authors.forename: Toshio
authors.initials: T
authors.lastname: Uchiumi
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D019843:Archaeal Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D017124:Conserved Sequence; D019281:Dimerization; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D011485:Protein Binding; D043902:Pyrococcus horikoshii / Q000235:genetics / Q000378:metabolism*; D012335:RNA, Ribosomal / Q000235:genetics; D012270:Ribosomes / Q000378:metabolism*; D016415:Sequence Alignment; D021241:Spectrometry, Mass, Electrospray Ionization