Compilation of 5S rRNA and 5S rRNA gene sequences (original) (raw)

Journal Article

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Institut für Biochemie, Freie Universität Berlin

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Thielallee 63, 14195 Berlin, Germany

*To whom correspondence should be addressed. Tel: +49 30 838 6405; Fax: +49 30 838 6403; Email: thy@chemie.fu-berlin.de

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1

Institute of Bioorganic Chemistry, Polish Academy of Sciences

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Noskowskiego 12/14, 61-704 Poznan, Poland

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Miroslawa Z. Barciszewska

1

Institute of Bioorganic Chemistry, Polish Academy of Sciences

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Noskowskiego 12/14, 61-704 Poznan, Poland

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1

Institute of Bioorganic Chemistry, Polish Academy of Sciences

,

Noskowskiego 12/14, 61-704 Poznan, Poland

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Received:

09 October 1996

Accepted:

10 October 1996

Published:

01 January 1997

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Thomas Specht, Maciej Szymanski, Miroslawa Z. Barciszewska, Jan Barciszewski, Volker A. Erdmann, Compilation of 5S rRNA and 5S rRNA gene sequences, Nucleic Acids Research, Volume 25, Issue 1, 1 January 1997, Pages 96–97, https://doi.org/10.1093/nar/25.1.96
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Abstract

The compilation of 5S rRNA and 5S rRNA gene nucleotide sequences as of 30 September 1996, contains a total of 1661 primary structures of 5S rRNAs or their genes, which is an increase of 928 new sequence entries over the last compilation. It covers sequences from 54 archaea, 449 eubacteria, 34 plastids, nine mitochondria and 430 eukaryotes. The databank uses the format of the EMBL Nucleotide Sequence Data Library complemented by a Sequence Alignment (SA) field including secondary structure information. The taxonomic classification of organisms was totally updated. Now the database is also available via anonymous FTP or WWW.

Introduction

The compilation provides aligned, annotated and phylogenetically ordered nucleotide sequences of prokaryotic and eukaryotic ribosomal 5S ribonucleic acids and their genes. 5S rRNA is a relatively small RNA molecule and has been subject to various studies with respect to its structure and biological function. This RNA species is a ubiquitous component of ribosomes of all living organisms. The nucleotide sequence of 5S rRNA is strongly conserved and provides substantial amount of data for the analysis of higher order structure relationships (2). 5S ribosomal RNA is the only known rRNA species that binds to ribosomal protein(s) before it is incorporated into the large ribosomal subunit both in eukaryotic and prokaryotic cells. In eukaryotes the 5S rRNA molecule binds only ribosomal protein L5, whereas in bacteria it interacts with up to three proteins, L5, L18 and L25 (3). The structure of the 5S rRNA molecule and its complexes with proteins have been analysed using chemical and enzymatic footprinting experiments and mutational studies (2). A better understanding of the nature of intramolecular interactions within the 5S rRNA, as well as the interaction between the nucleic acid and the protein components of its RNP complexes should extend our knowledge of the ribosomal assembly and RNA—protein interactions. To get a consistent picture of the structure—function relationships of 5S rRNA, the detailed knowledge concerning its structure is necessary. The aim of this work was to compile all currently known nucleotide sequences of 5S rRNAs and 5S rDNAs. It also includes the sequences that are not available from GenBank or EMBL data bases. We have also revised the taxonomic classification of organisms within the database.

Taxonomy

In comparison with the previous compilations (1,4,5,6) we have updated the taxonomic classification of organisms (Table 1). We have also noticed some inconsistences in the classification of organisms recorded in the EMBL and GenBank data entries. Therefore each record was checked and, when necessary, changed. In most cases the taxonomic classification was adapted towards the taxonomic browser of NCBI/GenBank, which can be accessed via WWW at: http://www3.ncbi.nlm.nih.gov/Taxonomy/tax.html

The Secondary Structure

The secondary structures of all 5S rRNAs consist of five helices which are connected by loops. Most differences are found in Helix D, which is well suited to distinguish between eukaryotes, eubacteria and archaea. The secondary structure can be found in the SA-field.

Database Access

The data files are available via anonymous FTP at ftp.fu-berlin.de in the directory /science/biochem/db/5SrRNA. All other information concerning 5S rRNA, as well as an individual sequence browser can be obtained via WWW at: http://rose.man.poznan.pl/5SData/5SRNA.htmlhttp://www.chemie.fu-berlin.de/fb_chemie/ibc/agerdmann/5S_rRNA.html

Table 1

Summary of all nucleotide sequences for 5S rRNA and 5S rDNA

Acknowledgements

We thank all those colleagues who have sent us their manuscripts saving us enormous time. On our WWW-servers we will create forms for direct submission of new 5S rRNA data. Suggestions, corrections and useful hints can also be sent via email to:

1. Thomas Specht (thy@chemie.fu-berlin.de)
2. Maciej Szymanski (mszyman@ibch.poznan.pl)

This work has been supported by the Deutsche Forschungsgemeinschaft (Gottfried Wilhelm Leibniz Prize, the Sonderforschungsbereich 344-C8), the Deutsche Agentur für Raumfahrtangelegenheiten GmbH, the Fonds der Chemischen Industrie e.V. and the Polish State Committee for Scientific Research.

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