Compilation of small ribosomal subunit RNA sequences

Abstract

INTRODUCTIONThe database on small ribosomal subunit RNA (further abbreviated as SSU rRNA) structure has more than doubled in size in one year's time and currently contains 927 aligned sequences. Table 1 only lists the 475 sequences (references 1-475) that were added to the database since publication of the last compilation (476). The latter should be consulted for data and references concerning the sequences entered previously. The total set of 927 entries now consists of 197 eukaryotic cytoplasmic, 21 archaeal, 625 bacterial, 21 plastidial, and 63 mitochondrial SSU rRNAs. This set includes partial sequences, but only if they satisfy the criterion defined in detail in the previous compilation (476) and in footnote (f) of Table 1, in short if the combined lengths of the sequenced segments corresponds to at least 70% of the Escherichia coli 16S rRNA sequence.Sequence alignment is based largely on the adopted secondary structure model, which in turn is corroborated by the observation of compensating substitutions in the alignment. Therefore, the secondary structure model can be gradually refined as more sequences become available. Some improvements to the secondary structure model for eukaryotic SSU rRNAs are described below. Fig. 1 shows the prokaryotic secondary structure model, applicable to SSU rRNAs from archaea, bacteria, plastids and mitochondria. The model of Fig. 2 applies to eukaryotic cytoplasmic SSU rRNAs. Areas of conserved primary and secondary structure are drawn in bold lines. Areas of variable primary and secondary structure, drawn in thin lines, are labelled VI to V9. Variability in secondary structure often consists in extension or reduction in size of helices in some species with respect to others. Long insertions present in a limited number of species result in the presence of extra helices, drawn in broken lines. SECONDARY STRUCTURE MODEL Prokaryotic and eukaryotic modelsThe prokaryotic model is identical to the one shown in the previous compilation (476), but the eukaryotic model has been adapted, the changes being enumerated below. The two models are distinguished, even though they have many helices in common, because helix P21, which usually forms variable area V4 of prokaryotic SSU rRNAs, apparently is not homologous to any of the helices E21-1 to E21-10 forming area V4 in eukaryotic SSU rRNAs.Helix numbering system Helices are given a different number if separated by a multibranched loop, (e.g. helices 9 and 10), by a pseudoknot loop (e.g. helices 1 and 2), or by a single stranded area that does not form a loop (e.g. helices 2 and 30). A single number is attributed to 48 'universal' helices, which are present in all hitherto known SSU rRNAs from archaea, bacteria, and plastids. They are also present in all known eukaryotic SSU rRNAs except that of the microsporidian Vairimorpha necatrix, which lacks helices 10, 11, and 44. Additional helices specific to the prokaryotic model ( Fig. 1) are given composite numbers of the form Pa-b, where a is the number of the preceding universal helix and b...

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The Evolution of Trypanosomes Infecting Humans and Primates

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