Database on the structure of small subunit ribosomal RNA

doi:10.1093/nar/27.1.179

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Nucleic Acids Research Pages 179-183

Database on the structure of small subunit ribosomal RNA
Contents Of The Database
Secondary Structure And Nucleotide Variability
Availability Of The Data
Acknowledgements
References

Database on the structure of small subunit ribosomal RNA

Yves Van de Peer, Elmar Robbrecht¹, Sybren de Hoog², An Caers, Peter De Rijk and Rupert De Wachter*

Departement Biochemie, Universiteit Antwerpen (UIA), Universiteitsplein 1, B-2610 Antwerpen, Belgium, ¹Nationale Plantentuin, Domein van Bouchout, B-1860 Meise, Belgium and ²Centraalbureau voor Schimmelcultures, PO Box 273, NL-3740 AG Baarn, The Netherlands

Received October 8, 1998; Accepted October 13, 1998

ABSTRACT

Over 11 500 complete or nearly complete sequences are now available from the Antwerp database on small subunit ribosomal RNA. All these sequences are aligned with one another on the basis of the adopted secondary structure model, which is corroborated by the observation of compensating substitutions in the alignment. Literature references, accession numbers and taxonomic information are also compiled. The database can be consulted via the World Wide Web at URL http://rrna.uia.ac.be/ssu/

CONTENTS OF THE DATABASE

In August 1998, the Antwerp small subunit (SSU) rRNA database contained 3166 eukaryotic, 7336 bacterial, 324 archaeal, 120 plastid and 601 mitochondrial sequences. The database comprises complete or nearly-complete sequences while partial SSU rRNA sequences are included only if the combined length of the sequenced segments amounts to at least 70% of the estimated chain length of the molecule. The chain length of a partially determined sequence is estimated by comparing it to a complete sequence of a presumed close relative. All SSU rRNA sequences are stored in the form of an alignment and contain the postulated secondary structure pattern in encoded form (see the rRNA website at URL http://rrna.uia.ac.be/ for detailed information).

Table 1 lists the different eukaryotic taxa and the number of representatives in the database for which the SSU rRNA sequence has been determined. The taxonomic classification of the animals is according to Brusca and Brusca (1). For the plants and the Fungi, we have chosen to extend the taxonomic information supplied up to the level of orders, contrary to previous papers describing the contents of the SSU rRNA database. The classification of vascular plants is according to Mabberley (2), while the classification of Bryopsida is according to Crosby and Magill (3). Additional classificatory information for the terrestrial plants was taken from Sitte et al. (4) and Farr et al. (5). On the rRNA website, taxonomic information regarding the family to which the plant species are classified will also be available. The classification of the `true' fungi or Eumycota is according to Hawksworth et al. (6), Kurtzman and Fell (7), and de Hoog and Guarro (8). The remaining eukaryotes, viz. the protoctists are classified according to Margulis et al. (9). Overall, species are included in the database under the binomial used for the publication of the sequence. We therefore refrained from doing any taxonomic name change, even when obviously needed.

Table 1. List of eukaryotic taxa represented in the database and number of their representatives (August 1998)
^aThe Metazoan taxa are listed in the same order as they appear in ref. 1.
^bThe number of sequences listed in the database is larger than the number of species, because for certain species multiple SSU rRNA sequences have been determined, usually by different authors. The sequences are not necessarily identical because they may have been determined for different varieties or strains of a species, or for different genes of the same organism. The number is listed for sequences of nuclear (N), mitochondrial (M) and plastid (P) origin.
^cExcept in the case of the plant phyla, taxa are ordered alphabetically.

Table 2 covers the prokaryotic SSU rRNA sequences. The classification of prokaryotes is, as before, based on the construction of evolutionary trees. New sequences retrieved from EMBL or GenBank, or from direct submissions, are aligned with their presumed closest relative. Evolutionary trees are then constructed by the neighbor-joining method (10), and according to the phylogenetic position observed, the species are assigned to one of the taxa previously described by Woese and coworkers (11,12) and our research group (13,14).

SECONDARY STRUCTURE AND NUCLEOTIDE VARIABILITY

Our SSU rRNA sequence alignment is based on two different secondary structure models. The first one is the prokaryotic model, which is applicable to Bacteria, Archaea, plastids and mitochondria, while the second one is the eukaryotic model applicable to all Eukaryotes. The two models are slightly different, each containing a number of structural elements specific for the group (see below). The prokaryotic model is essentially identical to those distributed by Gutell (15), but the model followed for eukaryotic SSU rRNAs includes a secondary structure pattern in certain variable areas left undefined in the models of the latter author.

Helices in the SSU rRNA secondary structure model are given a different number if separated by a multibranched loop (e.g., helices 9 and 10), by a pseudoknot loop (e.g., helices 1 and 2), or by a single stranded area that does not form a loop (e.g., helices 2 and 32). A single number is given to 50 universal helices, which are present in all SSU rRNAs from Archaea, Bacteria and plastids known to date. These 50 helices are also present in all known eukaryotic SSU rRNAs except in those of the microsporidians (such as Vairimorpha, Nosema, and relatives), where some of these helices are missing. Helix 11 is also missing in the trichomonads and relatives. Helices specific to the eukaryotic model are numbered Ea-b, where a is the number of the preceding universal helix and b sequentially numbers all helices inserted between universal helices a and a+1. Helices specific to the prokaryotic model are similarly given composite numbers of the form Pa-b. Mitochondrial sequences show extreme variability in length and in the number of helices present. Figure 1 shows the secondary structure model of the plastid SSU rRNA nucleotide sequence of Zea mays.

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