Collection of small subunit (16S- and 16S-like) ribosomal RNA structures

Inferring higher-order structure for complex RNA molecules, such as the ribosomal RNAs has relied primarily on comparative methods. Underlying these methods is the premise that molecules with different primary structure and similar functional characteristics have similar secondary and tertiary structure [Reviewed in: 1]. For these methods to be effective, the RNA molecules under study need to be sufficiently similar at the primary structure level to obtain good sequence alignments, however these same sequences also need to be proportionately different for positional covariance to occur, the indicator suggesting the existence of a basepair. The higher-order structure models for 16S rRNA have evolved in stages. Initially, with a small number of 16S rRNA sequences in hand, a minimal secondary structure was proposed. Increases in the number and diversity of available 16S rRNA sequences and paralleled with improvements in correlation analysis algorithms has lead to the continual refinement of this structure model. In the earlier stages only secondary structure pairings were identified. In contrast during the latter stages only minor refinements in these pairings occurred while several novel tertary and non-canonical pairing constraints were proposed [reviewed in: 2-3]. And now with over 2,200 16S and 16S-like rRNA available sequences spanning the three phylogenetic domains and the two organelles (Mitochondria and Chloroplast), detailed phylogenetic, structural, and structural evolution information is now being deciphered in great detail, although the resulting analysis from different groups is not always congruent. Over the years several groups have developed 16S rRNA secondary structure models. The current versions for each are fairly analogous with one another[2, 4-7], although this has not always been the case. And while the current differences are small, some are significant for the Escherichia coli and other Bacterial, Archaea, Eucarya, and mitochondrial structure models. These versions should also not be considered final as these models are expected to undergo minor revisions as the number and diversity of 16S and 16S-like sequences increases and is paralleled with continued improvements and alternative correlation analysis interpretations [8, unpublished work]. Over the next few years this collection, and the accompanying 23S rRNA (see Gutell, Gray, Schnare, this issue) will grow in size and detail. The complexity of structure and the evolutionary dimension of these structures presents us with a wonderful opportunity to investigate RNA structural motifs and map with some precision, the evolution of these RNAs and underlying RNA structural characteristics associated with different phylogenetic assemblages. This collection of structures should also be of value to the experimentalist studying rRNA structure and function. And equally valuable to those studying rRNA based phylogeny.