ABSTRACT
The SRPDB (Signal Recognition Particle Database) offers aligned SRP RNA and SRP
protein sequences, phylogenetically ordered and annotated. This release adds
three SRP RNA sequences (totaling 96 SRP RNA sequences) and 11 SRP protein
sequences (a total of 39 protein sequences from SRP9, SRP14, SRP19, SRP21,
SRP54, SRP68 or SRP72). Also downloadable are sample SRP RNA secondary
structure diagrams, a three-dimensional model of the human SRP RNA, search motifs and software.
The Signal Recognition Particle Database (SRPDB) is located at the University of
Texas Health Science Center at Tyler. It provides 96 aligned and annotated
sequences of SRP RNAs and 39 SRP protein sequences. Alignments were created
using the rules described in ref. (
1
), and the sequences are grouped and ordered according to the phylogeny derived
by the Ribosomal Database Project (
2
).
In order to update the SRP RNA alignment, we searched release 96 of GenBank (
3
) using the software PatScan (
4
) and a series of motifs that each describe the most conserved primary and
secondary structure features, with broad allowance for mismatches. Only four
new SRP RNAs were identified, one from
Oryza sativa
(Chittenden
et al
., unpublished), two identical ones from
Caulobacter crescentus
(an alpha-purple bacterium), and one from
Clostridium perfringens
(a low-GC Gram-positive bacterium). The structure of the latter, the gene of which
follows immediately after the 3'CCA sequence of a serine tRNA, is 70% similar to the SRP RNA from
Bacillus
, and has been implicated in sporulation (
5
).
The SRP RNA alignment is available as concatenated GenBank (
6
) and EMBL (
7
) entries with gaps inserted in the sequences, as a human readable text format,
and as printable PostScript where helices are numbered and highlighted. The
corresponding sequences are also available as separate GenBank and EMBL
entries. Representative SRP RNA secondary structure models (in PostScript format) are from
Bacillus subtilis
(Bacteria),
Halobacterium halobium
(Archaea) and
Canis
sp. (Eukaryota). A tentative three-dimensional model [(
8
) in PDB format] is offered for human SRP RNA.
New SRP protein sequences include human SRP9 (a total of four SRP9 sequences), a
canine SRP14 sequence and SRP19 from
Methanococcus jannaschii
. The latter was identified in the complete genome of
M.jannaschii
(
9
) as a polypeptide of 87 residues using the motif P-(SVCA)-Y-X(8)-E-G-R-X(10)-P (
10
). The existence of an archaeal SRP19 homolog (Fig.
1
) was predicted earlier from structural studies of the SRP19-SRP RNA complex (
11
,
12
) and is now confirmed.
Methanococcus jannaschii
also contains a homolog for SRP54 (
9
), but equivalents of SRP9, SRP14, SRP68 and SRP72 were not identified in our
search; these proteins therefore may be absent in the archaeal SRP. Other new
SRP54 sequences were from
Mycoplasma genitalium
, barley (
Hordeum vulgare
, three closely related sequences),
Caenorhabditis elegans
(a partial sequences that aligns near the C-terminus of SRP54), and human SRP54. The SRP72 sequence from
Saccharomyces cerevisiae
(
13
) was aligned. If possible, protein entries were linked to their primary source
at GenBank (
6
) or EBI (
7
). The SRP protein alignments are available in textual (ASCII) or PostScript
format.
PatScan, a flexible pattern matching program (
4
), is available together with the search motifs used to identify new sequences.
This enables anyone to repeat the search, and to change our pattern
definitions.
All data and software are freely accessible and downloadable: connect your World
Wide Web browser to the URL http://pegasus.uthct.edu/SRPDB/SRPDB.html. SRPDB
can also be accessed directly by anonymous ftp to `diana.uthct.edu'. (Currently
192.88.11.4; login with the name `anonymous', without the quotes, and give your
full electronic mail address as the password.) The complete SRPDB can be
downloaded from the same site as a single tar-file. Hardcopies of the alignments are available through written contact
or through e-mail to the authors at `zwieb{at}jason.uthct.edu'; however electronic
transfer is preferred. Please cite this article if your research is assisted by
the SRPDB.
Submission of SRP-related data will be accepted in any form. We will align submitted
sequences and return the alignment to the submitter in the requested format.
The submitter may request that the data not be released until after a given
date or upon notification. C.Z. can be contacted by e-mail at zwieb{at}jason.uthct.edu, and N.L. can be contacted by e-mail at niels{at}truth.mph.msu.edu.
We thank the investigators who have submitted data prior to publication. This
work was assisted by NIH grant GM-49034 to C.Z. and by the Center for Microbial Ecology at Michigan State
University. We also thank the Free Software Foundation and Larry Wall for their
excellent free software, and Kimberly Chittenden for critical reading of the
manuscript.
REFERENCES
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