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Structure of the complete bacterial SRP Alu domain.

Kempf G, Wild K, Sinning I - Nucleic Acids Res. (2014)

Bottom Line: The mammalian Alu domain is a protein-RNA complex, while prokaryotic Alu domains are protein-free with significant extensions of the RNA.The 5' region includes an extended loop-loop pseudoknot made of five consecutive Watson-Crick base pairs.Homology modeling with the human Alu domain in context of the ribosome shows that an additional lobe in the pseudoknot approaches the large subunit, while the absence of protein results in the detachment from the small subunit.

View Article: PubMed Central - PubMed

Affiliation: Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany.

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Related in: MedlinePlus

The bacterial SRP Alu domain. (A) Schematic representation of the mammalian, archaeal and bacterial SRP. ‘Long SRP RNA’ refers to the presence of a 6S RNA in many gram-positive bacteria, in contrast to the short 4.5S RNA in most gram-negative bacteria. Mammalian and archaeal SRP share a 7S RNA. The Alu RNA is highlighted in blue. (B) Constructs of the Bacillus subtilis Alu domain RNA. The S domain is replaced by a tetraloop at the end of helix 5 (gray). (C) Size-exclusion chromatography coupled with MALS of unfolded (black) and folded (red) Alu107 RNA. The lines correspond to the UV signal and the dots to the molar mass distribution at the respective peak. (D) Electrophoretic mobility shift assay demonstrating the homogeneous folding of Alu107 RNA and comparison with deletion construct Alu87 (shortened helix 5).
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Figure 1: The bacterial SRP Alu domain. (A) Schematic representation of the mammalian, archaeal and bacterial SRP. ‘Long SRP RNA’ refers to the presence of a 6S RNA in many gram-positive bacteria, in contrast to the short 4.5S RNA in most gram-negative bacteria. Mammalian and archaeal SRP share a 7S RNA. The Alu RNA is highlighted in blue. (B) Constructs of the Bacillus subtilis Alu domain RNA. The S domain is replaced by a tetraloop at the end of helix 5 (gray). (C) Size-exclusion chromatography coupled with MALS of unfolded (black) and folded (red) Alu107 RNA. The lines correspond to the UV signal and the dots to the molar mass distribution at the respective peak. (D) Electrophoretic mobility shift assay demonstrating the homogeneous folding of Alu107 RNA and comparison with deletion construct Alu87 (shortened helix 5).

Mentions: The signal recognition particle (SRP) plays an essential role in co-translational targeting of newly synthesized membrane proteins (1,2). SRP is a ribonucleoprotein complex conserved in all three kingdoms of life with a high diversity regarding composition and complexity (3). Eukaryotic SRP contains six proteins assembled on a 7SL RNA (4) and can be divided into two functional domains. While the S domain recognizes SRP targets through their N-terminal signal sequences as soon as they emerge from the ribosomal tunnel exit, the Alu domain imposes an elongation arrest by blocking the elongation factor entry site (5–8). By retarding translation, SRP prevents membrane proteins from being prematurely released from the ribosome before the ribosome-nascent chain complex (RNC) has correctly engaged with the translocation channel at the endoplasmic reticulum membrane (1,9). The Alu domain of higher eukaryotes is composed of the 5′ and 3′ regions of SRP RNA and the two Alu RNA-specific proteins SRP9/14 (Figure 1A). The proteins stabilize the complex tertiary structure of the Alu RNA and contribute to ribosome binding (10–12). In a cryo-EM structure of mammalian SRP bound to the RNC, the SRP9/14 proteins were shown to interact with the small ribosomal subunit, while the Alu RNA establishes a contact with the large ribosomal subunit (12,13). The structure of the Alu RNA is instructive also for understanding of the retrotransposable, repetitive Alu elements, which comprise more than 10% of the primate genome and are derived from the 7SL RNA (14–18). Despite their abundance, the precise roles of Alu elements are still poorly understood, and their function in gene regulation or as templates for the production of new exons is just emerging (18,19).


Structure of the complete bacterial SRP Alu domain.

Kempf G, Wild K, Sinning I - Nucleic Acids Res. (2014)

The bacterial SRP Alu domain. (A) Schematic representation of the mammalian, archaeal and bacterial SRP. ‘Long SRP RNA’ refers to the presence of a 6S RNA in many gram-positive bacteria, in contrast to the short 4.5S RNA in most gram-negative bacteria. Mammalian and archaeal SRP share a 7S RNA. The Alu RNA is highlighted in blue. (B) Constructs of the Bacillus subtilis Alu domain RNA. The S domain is replaced by a tetraloop at the end of helix 5 (gray). (C) Size-exclusion chromatography coupled with MALS of unfolded (black) and folded (red) Alu107 RNA. The lines correspond to the UV signal and the dots to the molar mass distribution at the respective peak. (D) Electrophoretic mobility shift assay demonstrating the homogeneous folding of Alu107 RNA and comparison with deletion construct Alu87 (shortened helix 5).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4231752&req=5

Figure 1: The bacterial SRP Alu domain. (A) Schematic representation of the mammalian, archaeal and bacterial SRP. ‘Long SRP RNA’ refers to the presence of a 6S RNA in many gram-positive bacteria, in contrast to the short 4.5S RNA in most gram-negative bacteria. Mammalian and archaeal SRP share a 7S RNA. The Alu RNA is highlighted in blue. (B) Constructs of the Bacillus subtilis Alu domain RNA. The S domain is replaced by a tetraloop at the end of helix 5 (gray). (C) Size-exclusion chromatography coupled with MALS of unfolded (black) and folded (red) Alu107 RNA. The lines correspond to the UV signal and the dots to the molar mass distribution at the respective peak. (D) Electrophoretic mobility shift assay demonstrating the homogeneous folding of Alu107 RNA and comparison with deletion construct Alu87 (shortened helix 5).
Mentions: The signal recognition particle (SRP) plays an essential role in co-translational targeting of newly synthesized membrane proteins (1,2). SRP is a ribonucleoprotein complex conserved in all three kingdoms of life with a high diversity regarding composition and complexity (3). Eukaryotic SRP contains six proteins assembled on a 7SL RNA (4) and can be divided into two functional domains. While the S domain recognizes SRP targets through their N-terminal signal sequences as soon as they emerge from the ribosomal tunnel exit, the Alu domain imposes an elongation arrest by blocking the elongation factor entry site (5–8). By retarding translation, SRP prevents membrane proteins from being prematurely released from the ribosome before the ribosome-nascent chain complex (RNC) has correctly engaged with the translocation channel at the endoplasmic reticulum membrane (1,9). The Alu domain of higher eukaryotes is composed of the 5′ and 3′ regions of SRP RNA and the two Alu RNA-specific proteins SRP9/14 (Figure 1A). The proteins stabilize the complex tertiary structure of the Alu RNA and contribute to ribosome binding (10–12). In a cryo-EM structure of mammalian SRP bound to the RNC, the SRP9/14 proteins were shown to interact with the small ribosomal subunit, while the Alu RNA establishes a contact with the large ribosomal subunit (12,13). The structure of the Alu RNA is instructive also for understanding of the retrotransposable, repetitive Alu elements, which comprise more than 10% of the primate genome and are derived from the 7SL RNA (14–18). Despite their abundance, the precise roles of Alu elements are still poorly understood, and their function in gene regulation or as templates for the production of new exons is just emerging (18,19).

Bottom Line: The mammalian Alu domain is a protein-RNA complex, while prokaryotic Alu domains are protein-free with significant extensions of the RNA.The 5' region includes an extended loop-loop pseudoknot made of five consecutive Watson-Crick base pairs.Homology modeling with the human Alu domain in context of the ribosome shows that an additional lobe in the pseudoknot approaches the large subunit, while the absence of protein results in the detachment from the small subunit.

View Article: PubMed Central - PubMed

Affiliation: Heidelberg University Biochemistry Center (BZH), INF 328, D-69120 Heidelberg, Germany.

Show MeSH
Related in: MedlinePlus