A compilation of large subunit (23S-like) ribosomal RNA sequences presented in a secondary structure format.

The compendium presented here is the immediate successor of the collection of large subunit (LSU; 23S-like) rRNA secondary structures compiled by Gutell and Fox [1] in 1988. As in [1], we present each LSU rRNA sequence in the form of a secondary structure, as it is this structure that is a fundamental aspect of the biological activity of the LSU rRNA molecule. As such, the secondary structure provides valuable information on phylogenetically conserved and variable regions, as well as data relating form to function. Often, especially when dealing with homologous LSU rRNAs that are very divergent in structure (e.g., mitochondrial LSU rRNAs), it is considerably easier to extract required information from comparisons of secondary structures than from comparisons of the corresponding primary sequences. As much as possible, we have attempted to configure all of these LSU rRNA secondary structures according to the E. coli 23S rRNA model, which may be regarded as the standard or prototype structure upon which the others are based. This format facilitates comparison of homologous structural features among the different LSU rRNAs. The current E. coli 23S rRNA secondary structure has been slightly revised from that in the previous compendium (see [2]). The database of LSU rRNA sequences has expanded rapidly over the last two years. The listing presented here includes 7 archaebacterial, 13 eubacterial, 16 eukaryotic cytoplasmic (nuclear-encoded), 8 plastid, and 27 mitochondrial LSU rRNA sequences. Newly modeled secondary structures not included in the previous compilation are indicated in the table. The basic premise of the comparative method is that all LSU rRNA sequences fold into a similar secondary structure. Thus, the process of configuring each newly determined sequence according to the existing secondary structure model tests the validity of the latter model, and extends it when novel compensatory base changes are found. At this time, we are confident of the basic secondary structure that is common to all 23S (and 23S-like) rRNA sequences. However, there remain regions of some LSU rRNAs that have yet to be structured into helical arrays, or that have been structured by others on the basis of minimal comparative information. It is these structures that will be subject to further refinement as additional primary structures from select phylogenetic groupings are determined. We anticipate that the majority of such changes will occur in the existing eukaryotic cytoplasmic and mitochondrial LSU rRNA secondary structures, in regions of the rRNA that are common only to those phylogenetic groups, or to certain divisions therein. The decision by the editors to change to electronic media presentation provides us with an opportunity to improve upon the previous LSU rRNA compilation. Starting with the current collection, the actual 23S rRNA secondary structures will not be published here. Instead, readers will find (i) a table of complete LSU rRNA sequences, grouped according to phylogenetic division and including GenBank/EMBL Accession Numbers, and (ii) a publication reference list for these sequences. The comprehensive set of LSU rRNA secondary structures may be obtained in one of two ways. Hardcopy printouts of this set will be available directly from us (inquiries should be directed to M.W.G. at the address listed at the end of this compendium). Individuals with access to the Internet telecommunications network and a laser printer capable of processing PostScriptTM files may elect to obtain such files of LSU rRNA secondary structures. These files will be available on the GenBank computer in the near future. Information concerning this on-line service should be directed to R.R.G. (E-mail and postal addresses as noted below).