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SRPDB


NAR Molecular Biology Database Collection entry number 248
Alm Rosenblad, M.1, Zwieb, C.2, Samuelsson, T.1
1Department of Medical Biochemistry, University of GÅ¡teborg, Box 440, SE-405 30 GÅ¡teborg, Sweden
2Department of Molecular Biology, The University of Texas Health Science Center at Tyler, 11937 US Highway 271, Tyler, TX 75708-3154, USA

Database Description

Signal recognition particle (SRP) is an ribonucleoprotein particle designed to recognize secretory signal sequences as they emerge from the ribosome. SRP associates with the SRP-receptor in the ER membrane, is released from the ribosome, and recycled (for review, see [1, 2]). To assist the understanding of the molecular details of this essential cellular function, the SRP database (SRPDB) provides sequences of SRP RNAs, SRP proteins, and the SRP receptor ordered alphabetically and phylogenetically with links to the primary sources, as well as a manually-checked alignments. The SRP RNA alignment serves to derive supported secondary structures and helps to evaluate potential tertiary interactions. SRPDB is maintained at the University of Texas Health Science Center at Tyler, Texas, accessible on the World Wide Web at the URL http://psyche.uthct.edu/dbs/SRPDB/SRPDB.html and at the European mirror at the University of Goteborg, Sweden (http://bio.lundberg.gu.se/dbs/SRPDB/SRPDB.html). A web interface is available where a nucleotide sequence can be submitted to predict SRP RNA genes.

Recent Developments

On October 2004, the SRPDB contained 418 SRP RNAs, more than twice the number of sequences as in the previous announcement. There is a comparable increase in the number of SRP protein sequences (SRP9, SRP14, SRP19, SRP54 (Ffh), SRP68, and SRP72), as well as of the SRP receptor alpha subunit and its FtsY homolog. Due to improved computational methods for identifying SRP RNA sequences in the genomes of protozoa and fungi [3] and the biochemical probing of the yeast SRP RNAs [4] it is now possible to infer reliable secondary structures for all SRP RNAs as indicated in an updated SRP RNA alignment.

Acknowledgements

We thank Florian MÃœller (Max-Planck-Institute for Molecular Genetics Berlin, Germany) for ERNA-3D software. This work was supported by NIH grant GM-49034 to C.Z.

References

[1] Nagai K, Oubridge C, Kuglstatter A, Menichelli E, Isel C, Jovine L. (2003). Structure, function and evolution of the signal recognition particle. EMBO J. 22:3479-3485.
[2] Doudna JA, Batey RT. (2004). Structural insights into the signal recognition particle. Annu. Rev. Biochem. 73:539-557.
[3] Rosenblad MA, Zwieb C, Samuelsson T. (2004). Identification and comparative analysis of components from the signal recognition particle in protozoa and fungi. BMC Genomics 5:5.
[4] Van Nues RW, Brown JD. (2004). Saccharomyces SRP RNA secondary structures: A conserved S-domain and extended Alu-domain. RNA 10:75-89.
[5] Rosenblad, M.A., Larsen, N., Samuelsson, T., and Zwieb, C. (2009) Kinship in the SRP RNA family. RNA Biol. 6, 508-516


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