BackgroundComparative analysis of RNA sequences is the basis for the detailed and accurate predictions of RNA structure and the determination of phylogenetic relationships for organisms that span the entire phylogenetic tree. Underlying these accomplishments are very large, well-organized, and processed collections of RNA sequences. This data, starting with the sequences organized into a database management system and aligned to reveal their higher-order structure, and patterns of conservation and variation for organisms that span the phylogenetic tree, has been collected and analyzed. This type of information can be fundamental for and have an influence on the study of phylogenetic relationships, RNA structure, and the melding of these two fields.ResultsWe have prepared a large web site that disseminates our comparative sequence and structure models and data. The four major types of comparative information and systems available for the three ribosomal RNAs (5S, 16S, and 23S rRNA), transfer RNA (tRNA), and two of the catalytic intron RNAs (group I and group II) are: (1) Current Comparative Structure Models; (2) Nucleotide Frequency and Conservation Information; (3) Sequence and Structure Data; and (4) Data Access Systems.ConclusionsThis online RNA sequence and structure information, the result of extensive analysis, interpretation, data collection, and computer program and web development, is accessible at our Comparative RNA Web (CRW) Site http://www.rna.icmb.utexas.edu. In the future, more data and information will be added to these existing categories, new categories will be developed, and additional RNAs will be studied and presented at the CRW Site.

INTRODUCTIONThis compilation is part of an on-going 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). GROWTH OF THE DATABASEThe 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. [1][2][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][5][6]). MODELS OF HIGHER-ORDER STRUCTURE As in previous compilationsThree 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 LSU rRNA structures are compared and against which they are modelled); (ii) Saccharomyces cerevisiae (yeast), a representative eucaryotic (nucleocytoplasmic) structure; and (iii) a 'minimalist' structure, typified by the unusually small mitochondrial LSU rRNA from the nematode worm, Caenorhabditis elegans. While the latter two structures exemplify the tpe of size v...

To obtain PostScriptTM files of LSU rRNA secondary structures via anonymous ftp on the Internet telecommunications network: ftp site: info.mcs.anl.gov directory: /pub/RDP/Contrib/RobinGutell

No abstract

Background The mitochondrial genome in the human malaria parasite Plasmodium falciparum is most unusual. Over half the genome is composed of the genes for three classic mitochondrial proteins: cytochrome oxidase subunits I and III and apocytochrome b . The remainder encodes numerous small RNAs, ranging in size from 23 to 190 nt. Previous analysis revealed that some of these transcripts have significant sequence identity with highly conserved regions of large and small subunit rRNAs, and can form the expected secondary structures. However, these rRNA fragments are not encoded in linear order; instead, they are intermixed with one another and the protein coding genes, and are coded on both strands of the genome. This unorthodox arrangement hindered the identification of transcripts corresponding to other regions of rRNA that are highly conserved and/or are known to participate directly in protein synthesis. Principal Findings The identification of 14 additional small mitochondrial transcripts from P. falcipaurm and the assignment of 27 small RNAs (12 SSU RNAs totaling 804 nt, 15 LSU RNAs totaling 1233 nt) to specific regions of rRNA are supported by multiple lines of evidence. The regions now represented are highly similar to those of the small but contiguous mitochondrial rRNAs of Caenorhabditis elegans . The P. falciparum rRNA fragments cluster on the interfaces of the two ribosomal subunits in the three-dimensional structure of the ribosome. Significance All of the rRNA fragments are now presumed to have been identified with experimental methods, and nearly all of these have been mapped onto the SSU and LSU rRNAs. Conversely, all regions of the rRNAs that are known to be directly associated with protein synthesis have been identified in the P. falciparum mitochondrial genome and RNA transcripts. The fragmentation of the rRNA in the P. falciparum mitochondrion is the most extreme example of any rRNA fragmentation discovered.

Background: Dinoflagellates comprise an ecologically significant and diverse eukaryotic phylum that is sister to the phylum containing apicomplexan endoparasites. The mitochondrial genome of apicomplexans is uniquely reduced in gene content and size, encoding only three proteins and two ribosomal RNAs (rRNAs) within a highly compacted 6 kb DNA. Dinoflagellate mitochondrial genomes have been comparatively poorly studied: limited available data suggest some similarities with apicomplexan mitochondrial genomes but an even more radical type of genomic organization. Here, we investigate structure, content and expression of dinoflagellate mitochondrial genomes.

No abstract

No abstract