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 nucleotide sequence of the gene coding for small ribosomal subunit RNA in the basidiomycete Ustilago maydis was determined. It revealed the presence of a group I intron with a length of 411 nucleotides. This is the third occurrence of such an intron discovered in a small subunit rRNA gene encoded by a eukaryotic nuclear genome. The other two occurrences are in Pneumocystis carinii, a fungus of uncertain taxonomic status, and Ankistrodesmus stipitatus, a green alga.The nucleotides of the conserved core structure of 101 group I intron sequences present in different genes and genome types were aligned and their evolutionary relatedness was examined. This revealed a cluster including all group I introns hitherto found in eukaryotic nuclear genes coding for small and large subunit rRNAs. A secondary structure model was designed for the area of the Ustilago maydis small ribosomal subunit RNA precursor where the intron is situated. It shows that the internal guide sequence pairing with the intron boundaries fits between two helices of the small subunit rRNA, and that minimal rearrangement of base pairs suffices to achieve the definitive secondary structure of the 18S rRNA upon splicing.

The complete small ribosomal subunit RNA (srRNA) sequence was determined for the red alga Porphyra umbilicalis and the basidiomycete Leucosporidium scottii, representing two taxa for which no srRNA sequences were hitherto known. These sequences were aligned with other published complete srRNA sequences of 58 eukaryotes. Evolutionary trees were reconstructed by a matrix optimization method from a dissimilarity matrix based on sections of the alignment that correspond to structurally conservative areas of the molecule that can be aligned unambiguously. The overall topology of the eukaryotic tree thus constructed is as follows: first there is a succession of early diverging branches, leading to a diplomonad, a microsporidian, a euglenoid plus kinetoplastids, an amoeba, and slime molds. Later, a nearly simultaneous radiation seems to occur into a number of taxa comprising the metazoa, the red alga, the sporozoa, the higher fungi, the ciliates, the green plants, plus some other less numerous groups. Because the red alga diverges late in the evolutionary tree, it does not seem to represent a very primitive organism as proposed on the basis of morphological and 5S rRNA sequence data. Asco- and basidiomycetes do not share a common ancestor in our tree as is generally accepted on the basis of conventional criteria. In contrast, when all alignment positions, rather than the more conservative ones, are used to construct the evolutionary tree, higher fungi do form a monophyletic cluster. The hypothesis that higher fungi and red algae might have shared a common origin has been put forward. Although the red alga and fungi seem to diverge at nearly the same time, no such relationship can be detected. The newly determined sequences can be fitted into a secondary structure model for srRNA, which is now relatively well established with the exception of uncertainties in a number of eukaryote-specific expansion areas. A specific structural model featuring a pseudoknot is proposed for one of these areas.