The Alu domain homolog of the yeast signal recognition particle consists of an Srp14p homodimer and a yeast-specific RNA structure

Strub, Katharina; Fornallaz, M; Bui, Nazarena

doi:10.1017/s1355838299991045

Cited by 24 publications

(37 citation statements)

References 44 publications

(54 reference statements)

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“…2C, panels 30-11 and 62-42). This stem-loop was previously noted in S. cerevisiae scR1 by Strub et al (1999), whose model incorporates the 5Ј 99 nt of the RNA (Fig. 9A inset).…”

Section: The Alu-domainsupporting

confidence: 72%

“…The high level of sequence conservation of this region of scR1 FIGURE 9. Secondary structures (A) S. cerevisiae scR1 (and other sensu stricto species) with the structure proposed by Strub et al (1999) for bases 1-99 inset at the left. The box at the top provides a key to the bases that differ from the S. cerevisiae sequence.…”

Section: Discussionmentioning

confidence: 99%

“…A structure for the Alu-domain of scR1 has been proposed, and a putative domain IV modeled (Althoff et al 1994;Strub et al 1999). We have now developed an internally consistent model for the whole of scR1 combining data from enzymatic probing, mutagenesis, and phylogenetic comparison (Figs.…”

Section: Introductionmentioning

confidence: 99%

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Saccharomyces SRP RNA secondary structures: A conserved S-domain and extended Alu-domain

Nues¹,

Brown²

2003

RNA

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The contribution made by the RNA component of signal recognition particle (SRP) to its function in protein targeting is poorly understood. We have generated a complete secondary structure for Saccharomyces cerevisiae SRP RNA, scR1. The structure conforms to that of other eukaryotic SRP RNAs. It is rod-shaped with, at opposite ends, binding sites for proteins required for the SRP functions of signal sequence recognition (S-domain) and translational elongation arrest (Alu-domain). Micrococcal nuclease digestion of purified S. cerevisiae SRP separated the S-domain of the RNA from the Alu-domain as a discrete fragment. The Alu-domain resolved into several stable fragments indicating a compact structure. Comparison of scR1 with SRP RNAs of five yeast species related to S. cerevisiae revealed the S-domain to be the most conserved region of the RNA. Extending data from nuclease digestion with phylogenetic comparison, we built the secondary structure model for scR1. The Alu-domain contains large extensions, including a sequence with hallmarks of an expansion segment. Evolutionarily conserved bases are placed in the Alu-and S-domains as in other SRP RNAs, the exception being an unusual GU 4 A loop closing the helix onto which the signal sequence binding Srp54p assembles (domain IV). Surprisingly, several mutations within the predicted Srp54p binding site failed to disrupt SRP function in vivo. However, the strength of the Srp54p-scR1 and, to a lesser extent, Sec65p-scR1 interaction was decreased in these mutant particles. The availability of a secondary structure for scR1 will facilitate interpretation of data from genetic analysis of the RNA.

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“…2C, panels 30-11 and 62-42). This stem-loop was previously noted in S. cerevisiae scR1 by Strub et al (1999), whose model incorporates the 5Ј 99 nt of the RNA (Fig. 9A inset).…”

Section: The Alu-domainsupporting

confidence: 72%

Section: Discussionmentioning

confidence: 99%

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Saccharomyces SRP RNA secondary structures: A conserved S-domain and extended Alu-domain

Nues¹,

Brown²

2003

RNA

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“…Trypanosomal SRP comprises a tRNA-like molecule that might substitute SRP9/14 for activity (Lustig et al 2005(Lustig et al , 2010. In yeast, the homodimeric complex of SRP14 has replaced the heterodimer complex in yeast species (Strub et al 1999;Mason et al 2000). K60, 61, and 64 in h9 are not conserved in the homologous positions of yeast Srp14p (Birse et al 1997;Brooks et al 2009) and the pentapeptide is also less conserved in the yeast Neurospora crassa (Fig.…”

Section: Discussionmentioning

confidence: 99%

Residues in SRP9/14 essential for elongation arrest activity of the signal recognition particle define a positively charged functional domain on one side of the protein

Mary

Scherrer²,

Huck³

et al. 2010

RNA

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The signal recognition particle (SRP) is a ubiquitous cytoplasmic ribonucleoprotein complex required for the cotranslational targeting of proteins to the endoplasmic reticulum (ER). In eukaryotes, SRP has to arrest the elongation of the nascent chains during targeting to ensure efficient translocation of the preprotein, and this function of SRP is dependent on SRP9/14. Here we present the results of a mutational study on the human protein h9/14 that identified and characterized regions and single residues essential for elongation arrest activity. Effects of the mutations were assessed both in cell-free translation/translocation assays and in cultured mammalian cells. We identified two patches of basic amino acid residues that are essential for activity, whereas the internal loop of SRP14 was found to be dispensable. One patch of important basic residues comprises the previously identified basic pentapetide KRDKK, which can be substituted by four lysines without loss of function. The other patch includes three lysines in the solvent-accessible a2 of h9. All essential residues are located in proximity in SRP9/14 and their basic character suggests that they serve as a positively charged platform for interactions with ribosomal RNA. In addition, they can all be lysines consistent with the hypothesis that they recognize their target(s) via electrostatic contacts, most likely with the phosphate backbone, as opposed to contacts with specific bases.

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“…The three-dimensional structure of the motif is characterized by a U-turn that is important for the binding of SRP9/14 (Weichenrieder et al 2000). This sequence also forms the major footprint of the SRP14 homodimer in the S. cerevisiae SRP (Strub et al 1999). Its conserved nature and broad distribution among the SRP sequences suggests that this sequence is required for the functionality of all of the larger SRP RNAs, even in organisms that lack homologs of SRP9/14.…”

Section: Srp Rna Featuresmentioning

confidence: 99%

A nomenclature for all signal recognition particle RNAs

Zwieb¹,

Nues²,

Rosenblad³

et al. 2004

RNA

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The signal recognition particle (SRP) is a cytosolic ribonucleoprotein complex that guides secretory proteins to biological membranes in all organisms. The SRP RNA is at the center of the structure and function of the SRP. The comparison of the growing number of SRP RNA sequences provides a rich source for gaining valuable insight into the composition, assembly, and phylogeny of the SRP. In order to assist in the continuation of these studies, we propose an SRP RNA nomenclature applicable to the three divisions of life.

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The Alu domain homolog of the yeast signal recognition particle consists of an Srp14p homodimer and a yeast-specific RNA structure

Abstract: The mammalian Alu domain of the signal recognition particle (SRP) consists of a heterodimeric protein SRP9/14 and the Alu portion of 7SL RNA and comprises the elongation arrest function of the particle. To define the domain in Saccharomyces cerevisiae SRP

Cited by 24 publications

References 44 publications

Saccharomyces SRP RNA secondary structures: A conserved S-domain and extended Alu-domain

Saccharomyces SRP RNA secondary structures: A conserved S-domain and extended Alu-domain

Residues in SRP9/14 essential for elongation arrest activity of the signal recognition particle define a positively charged functional domain on one side of the protein

A nomenclature for all signal recognition particle RNAs

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