A compilation of large subunit (23S and 23S-like) ribosomal RNA structures: 1993

INTRODUCTION This compilation is part of an ongoing effort to maintain a comprehensive and continually updated collection of large subunit (LSU; 23S and 23S-like) rRNA secondary structures and associated sequence and citation information. Table 1 gives a breakdown of the number and phylogenetic distribution of sequences currently in this LSU rRNA database. A listing of accession numbers for all complete LSU rRNA sequences now in the public domain is presented in Table 2. The reference list is an update of the information provided in the 1992 compilation [1]; here, we include only revised or new citations to LSU rRNA sequences. The complete bibliography of LSU rRNA sequences is available electronically, as is the complete listing of accession numbers presented in Table 1 (see below for instructions on how to obtain this information). The past year has seen the largest annual increase in the number of LSU rRNA sequences published and/or released through the EMBL, GenBank and DDBJ databanks (Table 1). This trend has also been apparent in each of the previous years we have monitored, emphasizing the steady increase in the rate at which LSU rRNA sequences are being determined. The rate of growth within each of the phylogenetic categories does vary, however. In the period covered by the present compilation, more than half (34/66) of the new sequences that appeared were (eu)bacterial ones. The second largest increase occurred in the Plastids category, due primarily to the release of 15 new Chlamydomonas chloroplast sequences. In the previous year, the greatest increases were in mitochondrial and eucaryotic (nuclear) sequences. Mitochondrial sequences still constitute the largest single category in the LSU rRNA database, as they have in every previous compilation. MODELS OF HIGHER-ORDER STRUCTURE As in previous compilations [1-3], each LSU rRNA primary sequence is presented in a two-dimensional format (the secondary structure) that underpins the biologically relevant conformation of an rRNA molecule. When LSU rRNA sequences are configured in this manner, phylogenetic information becomes readily apparent, as do patterns of variability and conservation in sequence and structure. At the same time, the secondary structure serves as an effective template for relating form to function. Principles for deducing higher-order structure have been enunciated in previous compilations [1-3] (see also [4-6]). Three phylogenetically and structurally distinct examples of current LSU rRNA secondary structures are presented in this communication. They are: (i) Escherichia coli, a typical (eu)bacterial structure (our reference standard, to which other …