title: Identification of 5-hydroxycytidine at position 2501 concludes characterization of modified nucleotides in E. coli 23S rRNA.
abstract: Complete characterization of a biomolecule's chemical structure is crucial in the full understanding of the relations between their structure and function. The dominating components in ribosomes are ribosomal RNAs (rRNAs), and the entire rRNA-but a single modified nucleoside at position 2501 in 23S rRNA-has previously been characterized in the bacterium Escherichia coli. Despite a first report nearly 20 years ago, the chemical nature of the modification at position 2501 has remained elusive, and attempts to isolate it have so far been unsuccessful. We unambiguously identify this last unknown modification as 5-hydroxycytidine-a novel modification in RNA. Identification of 5-hydroxycytidine was completed by liquid chromatography under nonoxidizing conditions using a graphitized carbon stationary phase in combination with ion trap tandem mass spectrometry and by comparing the fragmentation behavior of the natural nucleoside with that of a chemically synthesized ditto. Furthermore, we show that 5-hydroxycytidine is also present in the equivalent position of 23S rRNA from the bacterium Deinococcus radiodurans. Given the unstable nature of 5-hydroxycytidine, this modification might be found in other RNAs when applying the proper analytical conditions as described here.
authors: Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark.
authors: Jesper Foged
authors: JF
authors: Havelund
authors: Anders Michael Bernth
authors: AM
authors: Giessing
authors: Trine
authors: T
authors: Hansen
authors: Anette
authors: A
authors: Rasmussen
authors: Lincoln Greyson
authors: LG
authors: Scott
authors: Finn
authors: F
authors: Kirpekar
mesh_terms: D002853:Chromatography, Liquid; D003596:Cytosine / Q000031:analogs & derivatives* / Q000737:chemistry; D034301:Deinococcus / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics*; D013058:Mass Spectrometry; D008956:Models, Chemical; D009690:Nucleic Acid Conformation; D009711:Nucleotides / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics; D012338:RNA, Ribosomal, 23S / Q000737:chemistry* / Q000235:genetics*; D012270:Ribosomes
chemical_list: D009711:Nucleotides; D012329:RNA, Bacterial; D012338:RNA, Ribosomal, 23S; C017400:5-hydroxycytosine; D003596:Cytosine