Niels Larsen

The RDP (Ribosomal Database Project)

The Ribosomal Database Project (RDP) is a curated database that offers ribosome-related data, analysis services and associated computer programs. The offerings include phylogenetically ordered alignments of ribosomal RNA (rRNA) sequences, derived phylogenetic trees, rRNA secondary structure diagrams, and various software for handling, analyzing and displaying alignments and trees. The data are available via anonymous FTP (rdp.life.uiuc.edu), electronic mail (server@rdp.life.uiuc.edu), gopher (rdpgopher.life.uiuc.edu) and WWW (http://rdpwww.life.uiuc.edu/ ). The electronic mail and WWW servers provide ribosomal probe checking, approximate phylogenetic placement of user-submitted sequences, screening for possible chimeric rRNA sequences, automated alignment, and a suggested placement of an unknown sequence on an existing phylogenetic tree.

The ribosomal database project

The Ribosomal Database Project (RDP) is a curated database that offers ribosome data along with related programs and services. The offerings include phylogenetically ordered alignments of ribosomal RNA (rRNA) sequences, derived phylogenetic trees, rRNA secondary structure diagrams and various software packages for handling, analyzing and displaying alignments and trees. The data are available via ftp and electronic mail. Certain analytic services are also provided by the electronic mail server.

A new version of the RDP (Ribosomal Database Project)

The Ribosomal Database Project (RDP-II), previously described by Maidak et al. [ Nucleic Acids Res. (1997), 25, 109-111], is now hosted by the Center for Microbial Ecology at Michigan State University. RDP-II is a curated database that offers ribosomal RNA (rRNA) nucleotide sequence data in aligned and unaligned forms, analysis services, and associated computer programs. During the past two years, data alignments have been updated and now include >9700 small subunit rRNA sequences. The recent development of an ObjectStore database will provide more rapid updating of data, better data accuracy and increased user access. RDP-II includes phylogenetically ordered alignments of rRNA sequences, derived phylogenetic trees, rRNA secondary structure diagrams, and various software programs for handling, analyzing and displaying alignments and trees. The data are available via anonymous ftp (ftp.cme.msu. edu) and WWW (http://www.cme.msu.edu/RDP). The WWW server provides ribosomal probe checking, approximate phylogenetic placement of user-submitted sequences, screening for possible chimeric rRNA sequences, automated alignment, and a suggested placement of an unknown sequence on an existing phylogenetic tree. Additional utilities also exist at RDP-II, including distance matrix, T-RFLP, and a Java-based viewer of the phylogenetic trees that can be used to create subtrees.

The Ribosomal Database Project (RDP)

The Ribosomal Database Project (RDP) is a curated database that offers ribosome-related data, analysis services and associated computer programs. The offerings include phylogenetically ordered alignments of ribosomal RNA (rRNA) sequences, derived phylogenetic trees, rRNA secondary structure diagrams and various software for handling, analyzing and displaying alignments and trees. The data are available via anonymous ftp (rdp.life.uiuc.edu), electronic mail (server@rdp.life.uiuc.edu), gopher (rdpgopher.life.uiuc.edu) and World Wide Web (WWW)(http://rdpwww.life.uiuc.edu/). The electronic mail and WWW servers provide ribosomal probe checking, screening for possible chimeric rRNA sequences, automated alignment and approximate phylogenetic placement of user-submitted sequences on an existing phylogenetic tree.

Kinship in the SRP RNA family.

The signal recognition particle (SRP) is a ribonucleoprotein complex which participates in the targeting of protein to cellular membranes. The RNA component of the SRP has been found in all domains of life, but the size of the molecule and the number of RNA secondary structure elements vary considerably between the different phylogenetic groups. We continued our efforts to identify new SRP RNAs, compare their sequences, discover new secondary structure elements, conserved motifs, and other properties. We found additional proof for the variability in the apical loop of helix 8, and we identified several bacteria which lack all of their SRP components. Based on the distribution of SRP RNA features within the taxonomy, we suggest seven alignment groups: Bacteria with a small (4.5S) SRP RNA, Bacteria with a large (6S) SRP RNA, Archaea, Fungi (Ascomycota), Metazoa group, Protozoa group, and Plants. The proposed divisions improve the prediction of more distantly related SRP RNAs and provide a more inclusive representation of the SRP RNA family. Updates of the Rfam SRP RNA sequence collection are expected to benefit from the suggested groupings.

Archaeal rRNA Operons, Intron Splicing and Homing Endonucleases, RNA Polymerase Operons and Phylogeny

Summary Over the past decade our laboratory has had a strong interest in defining the phylogenetic status of the archaea. This has involved determining and analysing the sequences of operons of both rRNAs and RNA polymerases and it led to the discovery of the first archaeal rRNA intron. What follows is a description of some recent experiments and an appraisal of the significance of the earlier work.

Phylogenetic Analysis of the Archaeal Order of Sulfolobales Based on Sequences of 23S rRNA Genes and 16S/23S rDNA Spacers

Summary 23S rRNA genes from six members of the order of Sulfolobales, within the crenarchaeotal branch of the archaea, were cloned and sequenced. For each of the organisms Acidianus brierleyi, Acidianus infernus, Sulfolobus acidocaldarius, Sulfolobus solfataricus, Sulfolobus sbibatae and Stygiolobus azoricus the 23S rRNA gene is linked directly to that of 16S rRNA by a short (∼ 200 bp) spacer with no intervening tRNA gene and no closely linked 5S rRNA gene which is typical for the Crenarchaeota. A phylogenetic tree, derived from the 23S rRNA gene sequences, shows that the six organisms are closely related, compatible with their belonging to one Order, and cluster in three pairs: the two Acidianus species, S. sbibatae and S. solfataricus, and S. acidocaldarius and St. azoricus.

Towards microbial data integration

There are currently 100–200 microbiology-related databases in existence, although it is impossible to find answers to queries that span even a few of these. The Center for Microbial Ecology (CME) at Michigan State University seeks to change this situation by coordinating the creation of an Integrated Microbial Database (IMD), accessible through the World Wide Web (WWW). Such a system will contain up-to-date phylogeny and taxonomy, gene sequences (including genomes), biochemical data, metabolic models, ecological and phenotypic data. Current main obstacles to creation of an IMD are the lack of a single freely available organismal nomenclature with synonyms and the availability of much critical data. An IMD will have major impacts on microbial biology: currently intractable fundamental questions might be answered, experiments could be refocused, and new commercial possibilities created. An IMD should remain freely available and be created under an open development model.

The Primary and Secondary Structures of the 23S Ribosomal RNA from Thermoplasma acidophilum Define an Ancient Archaeal Divergence

Summary The nucleotide sequence of the 23S rRNA gene from the archaeon Thermoplasma acidophilum has been determined and a secondary-structure model of the rRNA molecule proposed. Both the primary and secondary structures of T. acidophilum 23S rRNA exhibit a number of characteristic archaeal features. Pairwise similarities were calculated for 14 archaeal 23S rRNA sequences and a phylogenetic tree derived from the corresponding distance measurements. The results show that T. acidophilum stems from an ancient, and possibly unique, divergence within the archaeal domain. This conclusion is supported by the observation that T. acidophilum 23S rRNA shares secondary-structure characteristics with both of the main archaeal lineages, the euryarchaeota (methanogens and halophiles) and the crenarchaeota (sulfurdependent thermoacidophiles), in roughly equal measure and that it possesses some unique features as well.