© 2001 Oxford University Press
Nucleic Acids Research, 2001, Vol. 29, No. 1
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SRPDB (Signal Recognition Particle Database) Jan Gorodkin, Bjarne Knudsen, Christian Zwieb1,* and Tore Samuelsson2 Department of Genetics and Ecology, The Institute of Biological Sciences, University of Aarhus, Building 540, Ny Munkegade, DK-8000 Aarhus C, Denmark, 1Department of Molecular Biology, The University of Texas Health Science Center at Tyler, 11937 US Highway 271, Tyler, TX 75708-3154, USA and 2Department of Medical Biochemistry, University of Göteborg, Box 440, SE-405 30 Göteborg, Sweden Received October 2, 2000; Accepted October 4, 2000
ABSTRACT
SRP FUNCTION
Signal recognition particle (SRP) is a stable cytoplasmic ribonucleoprotein complex that serves to translocate secretory proteins across membranes during translation. The SRP Database (SRPDB) provides compilations of SRP components, ordered alphabetically and phylogenetically. Alignments emphasize phylogeneticallysupported base pairs in SRP RNA and conserved residues in the proteins. Data are provided in various formats including a column arrangement for improved access and simplified computational usability. Included are motifs for identification of new sequences, SRP RNA secondary structure diagrams, 3-D models and links to high-resolution structures. This release includes 11 new SRP RNA sequences (total of 129), two protein SRP9 sequences (total of seven), two protein SRP14 sequences (total of 10), two protein SRP19 sequences (total of 16), 10 new SRP54 (ffh) sequences (total of 66), two protein SRP68 sequences (total of seven) and two protein SRP72 sequences (total of nine). Seven sequences of the SRP receptor α-subunit and its FtsY homolog (total of 51) are new. Also considered are β-subunit of SRP receptor, Flhf, Hbsu, CaM kinase II and cpSRP43. Access to SRPDB is at http://psyche.uthct.edu/dbs/ SRPDB/SRPDB.html and the European mirror http:// www.medkem.gu.se/dbs/SRPDB/SRPDB.html
Signal recognition particle (SRP) is a ribonucleoprotein particle for recognition of secretory signals as they emerge from the ribosome. SRP associates with the SRP receptor in the ER membrane, is released from the ribosome and recycled. Molecular details of this essential biological process are beginning to emerge (for reviews see 1,2).
SRPDB TABLE OF CONTENTS • • • •
About SRP, Overview, About SRPRDB, What’s New? SRP RNA, in alphabetical phylogenetic order SRP RNA alignment 2-D 3-D search motif lists SRP proteins: SRP9, SRP14, SRP19, Yeast SRP21, SRP54, SRP68, SRP72 • More protein: SRP receptor α subunit (FtsY), SRP receptor β subunit • Flhf Hbsu CaM kinase II cpSRP43 • Links, Disclaimer
SRP COMPONENTS SRP RNA, although variable in size, is present in every SRP and may interact directly with the signal peptide (3). Comparative sequence analysis has established up to eight RNA helices (numbered from 1 to 8) (4) to define the small domain (helices 2, 3, 4 and a portion of helix 5), and the large domain (the remaining helix 5 portion and helices 6, 7 and 8). Seven SRP proteins were identified (see Table of Contents, above), but SRP21 is present only in Saccharomyces cerevisiae (5). Protein SRP54 (called ffh in bacteria) is essential due to its ability to bind signal peptide and SRP RNA. Most bacteria contain an SRP composed of only Ffh and a 4.5S SRP RNA. Analysis of completed genomes indicates that archaea have an RNA similar to eucaryotic SRP RNA, but only two SRP proteins, SRP19 and SRP54 (6). The database includes information about SRP pathway-associated proteins [SRP receptor α (FtsY), SRP receptor β, Flhf and Hbsu] as well as CaM kinase II (REF) and cpSRP43 (REF). SRPDB DESCRIPTION SRPDB provides aligned, annotated and phylogenetically ordered sequences related to structure and function of SRP, organized for SRP RNA, SRP proteins and SRP receptor α (FtsY). Included is information about SRP receptor β, Flhf, Hbsu, CaM kinase II and cpSRP43. SRP RNAs Known SRP RNA sequences (7) were used as queries with BLASTN (8) to search GenBank (9). The pattern matcher program PATSCAN (available at http://www-c.mcs.anl.gov/ home/overbeek/PatScan/HTML/patscan.html) helped to identify SRP RNA-specific secondary structure elements. We have also developed a program (to be published elsewhere) which specifically identified SRP RNA helix 8. In combination with
*To whom correspondence should be addressed. Tel: +1 903 877 7689; Fax: +1 903 877 5731; Email:
[email protected]
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Mfold [Wisconsin Package Version 10.0, Genetics Computer Group (GCG), Madison, WI] this program found most of the new bacterial RNAs reported here. The 11 SRP RNA sequences were from Aeropyrum pernix, Campylobacter jejuni, Neisseria meningitidis strain MC58, Prochlorococcus sp., Pyrococcus abyssi, Streptococcus mutans, Streptomyces coelicolor, Ureaplasma urealyticum, Vibrio cholerae, Xylella fastidiosa and Zymomonas mobilis. The updated alignment was generated manually with BIOEDIT (http://www.mbio.ncsu.edu/ RNaseP/info/programs/BIOEDIT/bioedit.html) and confirmed the previously determined secondary structure features. A suite of programs developed recently (manuscript in preparation) was applied to check manually updated alignments for consistent base pair assignments and possible extension of stems. Alignments are provided in several formats including a column format which is easily managed by computer programs to assist in the manual update of RNA databases. A small number of 3-D SRP RNA models in PDB format were generated with ERNA-3D (10) and refined by energy minimization with VCMD (11). Structures, solved recently by X-ray diffraction or NMR are available in the links section. SRP proteins Sequences of known SRP protein were used as queries for BLASTP (8). We also developed a semi-automated procedure where Psi-blast was used to find homologous sequences in protein and nucleotide sequence databases. In the latter procedure, clustalw (12) was used to produce multiple alignments of the top-scoring entries shown at http://www.medkem.gu.se/srpdb. Homologs of SRP9, SRP14, SRP19, SRP68 and SRP72 for respective totals of 7, 10, 16, 7 and 9 sequences were identified in Arabidopsis thaliana and Drosophila melanogaster and including a Schizosaccharomyces pombe SRP14 homolog. SRP72 was found in Leishmania major, previously annotated as a hypothetical protein fragment (accession CAB55514). New SRP54 sequences were from Acidithiobacillus ferrooxidans, Buchnera aphidicola, C. jejuni, Chlamydia muridarum, Chlamydia pneumoniae, L.major, N.meningitidis (two strains), Ureaplasma urealyticum, V.cholera and X.fastidiosa for a total of 66. SRP receptor proteins New SR α proteins in SRPDB were from V.cholerae, X.fastidosa, C.jejeuni, N.meningitidis (two different strains MC58 and Z2491), Caulobacter crescentus, C.muridarum and S.pombe. SRP affiliated proteins Shown is a preliminary alignment of the β subunit of the SRP receptor (see also http://www.medkem.gu.se/srpdb), as well as references and links about Flhf, Hbsu, CaM kinase II and cpSRP43.
ACCESS Data are accessible freely for research purposes at http:// psyche.uthct.edu/dbs/SRPDB/SRPDB.html and the European mirror site (http://www.medkem.gu.se/dbs/SRPDB/SRPDB.html). Hardcopies of the alignments are available by email request to the corresponding author at
[email protected] or through written contact. The first two authors can be reached at the email address
[email protected] and
[email protected], respectively, and the last author at
[email protected]. Please cite this article in research projects assisted by use of SRPDB. ACKNOWLEDGEMENTS We thank Florian Müller for ERNA-3D, Ingolf Sommer for VCMD software and Jody Burks for help with BLAST searches. This work is supported by NIH grant GM-49034 to C.Z. J.G. is supported by the Danish Technical Research Council. REFERENCES 1. Lütcke,H. (1995) Signal recognition particle (SRP), a ubiquitous initiator of protein translocation. Eur. J. Biochem., 228, 531–550. 2. Bui,N. and Strub,K. (1999) Biol. Chem., 380, 135–145. 3. Batey,R.T., Rambo,R.P., Lucast,L., Rha,B. and Doudna,J.A. (2000) Crystal structure of the ribonucleoprotein core of the signal recognition particle. Science, 287, 1232–1239. 4. Larsen,N. and Zwieb,C. (1991) SRP-RNA sequence alignment and secondary structure. Nucleic Acids Res., 19, 209–215. 5. Brown,J.D., Hann,B.C., Medzihradszky,K.F., Niwa,M., Burlingame,A.L. and Walter,P. (1994) Subunits of the Saccharomyces cerevisiae signal recognition particle required for its functional expression. EMBO J., 13, 4390–4400. 6. Bhuiyan,S., Gowda,K., Hotokezaka,H. and Zwieb,C. (2000) Assembly of archaeal signal recognition particle from recombinant components. Nucleic Acids Res., 28, 1365–1373. 7. Zwieb,C. and Samuelsson,T. (2000) SRPDB (Signal Recognition Particle Database). Nucleic Acids Res., 28, 171–172. 8. Altschul,S.F., Madden,T.L., Schäffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389–3402. 9. Benson,D.A., Karsch-Mizrachi,I., Lipman,D.J., Ostell,J., Rapp,B.A. and Wheller,DL. (2000) GenBank. Nucleic Acids Res., 28, 15–18. 10. Müller,F., Döring,T., Erdemir,T., Greuer,B., Jünke,N., Osswald,M., Rinke-Appel,L., Stade,K., Thamm,S. and Brimacombe,R. (1995) Getting closer to an understanding of the three-dimensional structure of ribosomal RNA. Biochem. Cell Biol., 73, 767–773. 11. Sommer,I. and Brimacombe,R. (2000) Methods for refining interactively established models of ribosomal RNA towards a physico-chemically plausible structure. J. Comput. Chem., in press. 12. Higgins,D.G., Thompson,J.D. and Gibson,T.J. (1996) Using CLUSTAL for multiple sequence alignments., Methods Enzymol., 266, 383–402.
