The Small Subunit rRNA Modification Database

Abstract

The Small Subunit rRNA Modification Database provides a listing of reported post-transcriptionally modified nucleosides and sequence sites in small subunit rRNAs from bacteria, archaea and eukarya. Data are compiled from reports of full or partial rRNA sequences, including RNase T1 oligonucleotide catalogs reported in earlier literature in studies of phylogenetic relatedness. Options for data presentation include full sequence maps, some of which have been assembled by database curators with the aid of contemporary gene sequence data, and tabular forms organized by source organism or chemical identity of the modification. A total of 32 rRNA sequence alignments are provided, annotated with sites of modification and chemical identities of modifications if known, with provision for scrolling full sequences or user-dictated subsequences for comparative viewing for organisms of interest. The database can be accessed through the World Wide Web at http://medlib.med.utah.edu/SSUmods.

Figure 1

Chemical structures of presently known post-transcriptionally modified nucleosides from rRNA. A, archaea; B, bacteria; and E, eukarya. Symbols: m¹A, 1-methyladenosine; m²A, 2-methyladenosine; m⁶A, N⁶-methyladenosine; Am, 2′-O-methyladenosine; m⁶₂A, N⁶,N⁶-dimethyladenosine; Im, 2′-O-methylinosine; m³C, 3-methylcytidine; m⁴C, N⁴-methlycytidine; m⁵C, 5-methlycytidine; Cm, 2′-O-methylcytidine; ac⁴C, N⁴-acetylcytidine; m⁴Cm, N⁴,2′-O-dimethylcytidine; m⁴₂Cm, N⁴,N⁴,2′-O-trimethylcytidine; hm⁵C, 5-hydroxymethylcytidine; ac⁴Cm, N⁴-acetyl-2′-O-methylcytidine; m¹G, 1-methylguanosine; m²G, N²-methylguanosine; m⁷G, 7-methylguanosine; Gm, 2′-O-methylguanosine; m²₂G, N²,N²-dimethylguanosine; Ψ, pseudouridine; D, dihydrouridine; m³U, 3-methyluridine; m⁵U, 5-methyluridine; cm⁵U, 5-carboxymethyluridine; Um, 2′-O-methyluridine; m¹Ψ, 1-methylpseudouridine; m³Ψ, 3-methylpseudouridine; Ψm, 2′-O-methylpseudouridine; acp³U, 3-(3-amino-3-carboxypropyl)uridine; and m¹acp³Ψ, 1-methyl-3-(3-amino-3-carboxypropyl)pseudouridine.