Identities and Phylogenetic Comparisons of Posttranscriptional Modifications in 16 S Ribosomal RNA fromHaloferax volcanii

Jeffrey A. Kowalak, Eveline Bruenger, Pamela F. Crain, James A. McCloskey
2000 Journal of Biological Chemistry  
Small subunit (16 S) rRNA from the archaeon Haloferax volcanii, for which sites of modification were previously reported, was examined using mass spectrometry. A census of all modified residues was taken by liquid chromatography/electrospray ionization-mass spectrometry analysis of a total nucleoside digest of the rRNA. Following rRNA hydrolysis by RNase T 1 , accurate molecular mass values of oligonucleotide products were measured using liquid chromatography/electrospray ionization-mass
more » ... ization-mass spectrometry and compared with values predicted from the corresponding gene sequence. Three modified nucleosides, distributed over four conserved sites in the decoding region of the molecule, were characterized: 3-(3-amino-3-carboxypropyl)uridine-966, N 6 -methyladenosine-1501, and N 6 ,N 6 -dimethyladenosine-1518 and -1519 (all Escherichia coli numbering). Nucleoside 3-(3-amino-3-carboxypropyl)uridine, previously unknown in rRNA, occurs at a highly conserved site of modification in all three evolutionary domains but for which no structural assignment in archaea has been previously reported. Nucleoside N 6 -methyladenosine, not previously placed in archaeal rRNAs, frequently occurs at the analogous location in eukaryotic small subunit rRNA but not in bacteria. H. volcanii small subunit rRNA appears to reflect the phenotypically low modification level in the Crenarchaeota kingdom and is the only cytoplasmic small subunit rRNA shown to lack pseudouridine.
doi:10.1074/jbc.m002153200 pmid:10818097 fatcat:xd7kajv5anewjpbbjje74qvyta