title: Modifications in Thermus thermophilus 23 S ribosomal RNA are centered in regions of RNA-RNA contact.
abstract: Ribosomal RNA from all organisms contains post-transcriptionally modified nucleotides whose function is far from clear. To gain insight into the molecular interactions of modified nucleotides, we investigated the modification status of Thermus thermophilus 5 S and 23 S ribosomal RNA by mass spectrometry and chemical derivatization/primer extension. A total of eleven modified nucleotides was found in 23 S rRNA, of which eight were singly methylated nucleotides and three were pseudouridines. These modified nucleotides were mapped into the published three-dimensional ribosome structure. Seven of the modified nucleotides located to domain IV, and four modified nucleotides located to domain V of the 23 S rRNA. All posttranscriptionally modified nucleotides map in the center of the ribosome, and none of them are in contact with ribosomal proteins. All except one of the modified nucleotides were found in secondary structure elements of the 23 S ribosomal RNA that contact either 16 S ribosomal RNA or transfer RNA, with five of these nucleotides physically involved in intermolecular RNA-RNA bridges. These findings strongly suggest that the post-transcriptional modifications play a role in modulating intermolecular RNA-RNA contacts, which is the first suggestion on a specific function of endogenous ribosomal RNA modifications.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.
authors.forename: Jonas
authors.initials: J
authors.lastname: Mengel-Jørgensen
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.
authors.forename: Søren Skov
authors.initials: SS
authors.lastname: Jensen
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.
authors.forename: Anette
authors.initials: A
authors.lastname: Rasmussen
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.
authors.forename: Jacob
authors.initials: J
authors.lastname: Poehlsgaard
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.
authors.forename: Jens Jørgen Lønsmann
authors.initials: JJL
authors.lastname: Iversen
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark. Electronic address: f.kir@bmb.sdu.dk.
authors.forename: Finn
authors.initials: F
authors.lastname: Kirpekar
mesh_terms: D001665:Binding Sites; D013058:Mass Spectrometry; D009711:Nucleotides / Q000032:analysis; D020401:Primed In Situ Labeling; D012323:RNA Processing, Post-Transcriptional / Q000502:physiology*; D012336:RNA, Ribosomal, 16S / Q000378:metabolism; D012338:RNA, Ribosomal, 23S / Q000378:metabolism*; D012343:RNA, Transfer / Q000378:metabolism; D016963:Thermus thermophilus / Q000235:genetics*
chemical_list: D009711:Nucleotides; D012336:RNA, Ribosomal, 16S; D012338:RNA, Ribosomal, 23S; D012343:RNA, Transfer