SRP-RNA sequence alignment and secondary structure

Larsen, Niels; Zwieb, Christian W

doi:10.1093/nar/19.2.209

Cited by 178 publications

(205 citation statements)

References 43 publications

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“…SRP RNA: SRP RNA has a long, double helical structure with one pseudoknot structure close to the 5' end [30], which can be viewed as 'kissing hairpins'. Our structure prediction is based on the alignment of 8 archaeal sequences.…”

Section: Resultsmentioning

confidence: 99%

Prediction of consensus RNA secondary structures including pseudoknots

Witwer

Hofacker²,

Stadler³

2004

IEEE/ACM Trans. Comput. Biol. and Bioinf.

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Most functional RNA molecules have characteristic structures that are highly conserved in evolution. Many of them contain pseudoknots. Here we present a method for computing the consensus structures including pseudoknots based on alignments of a few sequences. The algorithm combines thermodynamic and covariation information to assign scores to all possible base pairs, the base pairs are chosen with the help of the maximum weighted matching algorithm. We applied our algorithm to five different types of RNA known to contain pseudoknots. All pseudoknots were predicted correctly, and more than 85% of the base pairs were identified.

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Section: Resultsmentioning

confidence: 99%

Prediction of consensus RNA secondary structures including pseudoknots

Witwer

Hofacker²,

Stadler³

2004

IEEE/ACM Trans. Comput. Biol. and Bioinf.

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“…The signal recognition particle (SRP) functions in cotranslational targeting of ribosomes synthesizing proteins with an N-terminal targeting signal to the membrane of the endoplasmic reticulum (ER) in eukaryotes and to the plasma membrane in prokaryotes (Walter & Johnson, 1994;Rapoport et al+, 1996;de Gier et al+, 1997)+ SRP recognizes an N-terminal targeting peptide emerging from the translating ribosomes, and, subsequently, the ribosome-SRP complex binds to the SRP receptor at the membrane+ Compared to mammalian SRP (Walter & Blobel, 1983), bacterial SRP is of simpler composition and consists of one RNA (4+5S RNA) and one protein (Ffh), which share homologies with their respective eukaryotic functional counterparts, 7S RNA (Poritz et al+, 1988) and SRP54 protein (Bernstein et al+, 1989;Römisch et al+, 1989)+ The majority of proteins secreted from bacteria appears to be exported posttranslationally by the SecB pathway, and the SRP pathway may be used for a few proteins only+ However, the SRP pathway in Escherichia coli is essential for membrane insertion of several inner membrane proteins (Ulbrandt et al+, 1997;Beck et al+, 2000), and the SRP and SecB pathways use the same translocon for protein translocation (de Gier et al+, 1998;Valent et al+, 1998)+ Ffh and the bacterial SRP receptor, FtsY, belong to the group of SRP-related GTPases+ Their G domains contain an insertion, I box, in the effector loop, and an N-terminal four-helix N domain that is closely packed against the G domain (Freymann et al+, 1997;Montoya et al+, 1997)+ The M domain of Ffh contains the binding sites for the signal sequence and the SRP RNA (Keenan et al+, 1998)+ The structure of the M domain of human SRP54 is similar (Clemons et al+, 1999)+ SRP and FtsY were reported to moderately stimulate each other's GTPase activity (Powers & Walter, 1995), and a conformational change in the I box region of FtsY upon binding to SRP was demonstrated by fluorescence measurements (Jagath et al+, 2000)+ Eukaryotic SRP RNA (7S RNA) can be divided into four structural domains (I-IV) (Poritz et al+, 1988) or eight helices (Larsen & Zwieb, 1991), of which the most conserved domain IV (or helix 8) is present in all SRP RNAs, including 4+5S RNA from E. coli. The structure of an RNA fragment comprising domain IV of E. coli 4+5S RNA has been determined by NMR (Schmitz et al+, 1999a(Schmitz et al+, , 1999b)+ Genetic and bioch...…”

Section: Introductionmentioning

confidence: 97%

Important role of the tetraloop region of 4.5S RNA in SRP binding to its receptor FtsY

Jagath

Matassova

Leeuw³

et al. 2001

RNA

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Binding of Escherichia coli signal recognition particle (SRP) to its receptor, FtsY, requires the presence of 4.5S RNA, although FtsY alone does not interact with 4.5S RNA. In this study, we report that the exchange of the GGAA tetraloop sequence in domain IV of 4.5S RNA for UUCG abolishes SRP-FtsY interaction, as determined by gel retardation and membrane targeting experiments, whereas replacements with other GNRA-type tetraloops have no effect. A number of other base exchanges in the tetraloop sequence have minor or intermediate inhibitory effects. Base pair disruptions in the stem adjacent to the tetraloop or replacement of the closing C-G base pair with G-C partially restored function of the otherwise inactive UUCG mutant. Chemical probing by hydroxyl radical cleavage of 4.5S RNA variants show that replacing GGAA with UUCG in the tetraloop sequence leads to structural changes both within the tetraloop and in the adjacent stem; the latter change is reversed upon reverting the C-G closing base pair to G-C. These results show that the SRP-FtsY interaction is strongly influenced by the structure of the tetraloop region of SRP RNA, in particular the tetraloop stem, and suggest that both SRP RNA and Ffh undergo mutual structural adaptation to form SRP that is functional in the interaction with the receptor, FtsY.

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“…The search motifs can be downloaded from our ftp server (see below), so that others may search new data or modify the motifs. The new SRP RNAs were aligned using the rules previously described (6).…”

Section: Descriptionmentioning

confidence: 99%

The Signal Recognition Particle Database (SRPDB)

Zwieb¹,

Larsen²

1997

Nucleic Acids Research

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The Signal Recognition Particle Database (SRPDB) provides aligned SRP RNA and SRP protein sequences, annotated and phylogenetically ordered. The current release includes 93 RNAs and 29 proteins representing SRP9, SRP14, SRP19, SRP21, SRP54, SRP68 and SRP72. The SRPDB can be downloaded and is accessible via the World Wide Web. DESCRIPTIONThe signal recognition particle database (SRPDB), located at The University of Texas Health Science Center at Tyler, currently offers 93 aligned and annotated sequences of SRP associated RNAs. The sequences are ordered according to the phylogeny derived by the Ribosomal Database Project (1) from the corresponding small subunit ribosomal RNAs (SSU RNAs). Included are also a total of 29 SRP related proteins. Representative SRP RNA secondary structure diagrams are provided, one from Bacillus subtilis (Bacteria), Halobacterium halobium (Archaea) and Canis sp. (Eucaryotes).In order to update SRPDB we screened the EMBL Data Library (2), current as of September 22, 1995, for sequences annotated as SRP-related using the Sequence Retrieval System (SRS; 3). In addition, we used a local copy of the program PatScan (4) to search all sequences in EMBL for matches against a motif characteristic for the SRP sequences that were part of the previous release of SRPDB (5). PatScan searches may be performed at the World Wide Web address http://www.mcs.anl.gov/home/papka/ ROSS/patscan.html. The search motifs can be downloaded from our ftp server (see below), so that others may search new data or modify the motifs. The new SRP RNAs were aligned using the rules previously described (6).Only six new SRP RNAs were identified. Two were from Caenorhabditis elegans genomic sequences (Cosmid B0285: approximate position 38 785-39 085; Cosmid CER144: approximate position 33 863-33 563 on the non-coding strand) submitted to EMBL, but without annotation of SRP RNAs. Four SRP RNAs have so far been identified in the genomic sequences of C.elegans. They all differ at between one and six positions. Two new cultivars of Humulus are included. In the newly released complete genomic sequence of Haemophilus influenzae (7) we identified an SRP RNA analog (4.5S RNA) from approximate position 1 223 294-1 223 407, not previously annotated. This sequence seems most similar to those of Escherichia and Pseudomonas (in agreement with the SSU RNA phylogeny) and it also lacks helices 1, 2, 3, 4 and 5. The SRP RNA from Listeria monocytogenes (8) includes helix 5, but does not align well with helices 1, 2 or 3 (which are supported by compensating changes among Bacillus species and all nine Archaea representatives. Comparative evidence is needed to determine the folding pattern for Listeria SRP RNA near the 5′ end. While these new sequences exhibit a few supportive compensatory changes, none of them provide comparative disproof for any of the known pairings.There are nine new SRP proteins in SPRDB (a total of 29) since its previous announcement: Mouse SRP9, Drosophila and rice SRP19, yeast SRP21, an Arabidopsis chloroplast SR...

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SRP-RNA sequence alignment and secondary structure

Cited by 178 publications

References 43 publications

Prediction of consensus RNA secondary structures including pseudoknots

Prediction of consensus RNA secondary structures including pseudoknots

Important role of the tetraloop region of 4.5S RNA in SRP binding to its receptor FtsY

The Signal Recognition Particle Database (SRPDB)

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