SRP RNA Remodeling by SRP68 Explains Its Role in Protein Translocation

Grotwinkel, J.T.; Wild, Klemens; Segnitz, Bernd; Sinning, Irmgard

doi:10.1126/science.1249094

Cited by 42 publications

(52 citation statements)

References 55 publications

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“…The N-terminal SRP68 RNA-binding domain (RBD) locates to a central RNA three-way junction between RNA helices 5, 6 and 8 (22). SRP68 binding to the RNA kinks the S domain RNA and remodels the nearby 5f-loop (23). Kinking is important for ribosome interaction at the previously described ‘C4-contact’ (24), while 5f-loop remodeling might activate the targeting complex as described in E. coli (7,8).…”

Section: Introductionmentioning

confidence: 99%

Structures of human SRP72 complexes provide insights into SRP RNA remodeling and ribosome interaction

Becker¹,

Lapouge²,

Segnitz³

et al. 2016

Nucleic Acids Res

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Co-translational protein targeting and membrane protein insertion is a fundamental process and depends on the signal recognition particle (SRP). In mammals, SRP is composed of the SRP RNA crucial for SRP assembly and function and six proteins. The two largest proteins SRP68 and SRP72 form a heterodimer and bind to a regulatory site of the SRP RNA. Despite their essential roles in the SRP pathway, structural information has been available only for the SRP68 RNA-binding domain (RBD). Here we present the crystal structures of the SRP68 protein-binding domain (PBD) in complex with SRP72-PBD and of the SRP72-RBD bound to the SRP S domain (SRP RNA, SRP19 and SRP68) detailing all interactions of SRP72 within SRP. The SRP72-PBD is a tetratricopeptide repeat, which binds an extended linear motif of SRP68 with high affinity. The SRP72-RBD is a flexible peptide crawling along the 5e- and 5f-loops of SRP RNA. A conserved tryptophan inserts into the 5e-loop forming a novel type of RNA kink-turn stabilized by a potassium ion, which we define as K+-turn. In addition, SRP72-RBD remodels the 5f-loop involved in ribosome binding and visualizes SRP RNA plasticity. Docking of the S domain structure into cryo-electron microscopy density maps reveals multiple contact sites between SRP68/72 and the ribosome, and explains the role of SRP72 in the SRP pathway.

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Section: Introductionmentioning

confidence: 99%

Structures of human SRP72 complexes provide insights into SRP RNA remodeling and ribosome interaction

Becker¹,

Lapouge²,

Segnitz³

et al. 2016

Nucleic Acids Res

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“…For example, Arrc06 is a widely distributed housekeeping RNA that is the functional RNA component of the signal recognition particle (SRP) that delivers nascent peptides to their proper destination (Grotwinkel et al 2014). Also very conserved and widespread, but with activities not related to the interaction with proteins, are the RNAs Arrc15 and Arrc23.…”

Section: Housekeeping Regulatory Rnasmentioning

confidence: 99%

A computational strategy for the search of regulatory small RNAs in Actinobacillus pleuropneumoniae

Rossi

Bossé

et al. 2016

RNA

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Bacterial regulatory small RNAs (sRNAs) play important roles in gene regulation and are frequently connected to the expression of virulence factors in diverse bacteria. Only a few sRNAs have been described for Pasteurellaceae pathogens and no in-depth analysis of sRNAs has been described for Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia, responsible for considerable losses in the swine industry. To search for sRNAs in A. pleuropneumoniae, we developed a strategy for the computational analysis of the bacterial genome by using four algorithms with different approaches, followed by experimental validation. The coding strand and expression of 17 out of 23 RNA candidates were confirmed by Northern blotting, RT-PCR, and RNA sequencing. Among them, two are likely riboswitches, three are housekeeping regulatory RNAs, two are the widely studied GcvB and 6S sRNAs, and 10 are putative novel trans-acting sRNAs, never before described for any bacteria. The latter group has several potential mRNA targets, many of which are involved with virulence, stress resistance, or metabolism, and connect the sRNAs in a complex gene regulatory network. The sRNAs identified are well conserved among the Pasteurellaceae that are evolutionarily closer to A. pleuropneumoniae and/or share the same host. Our results show that the combination of newly developed computational programs can be successfully utilized for the discovery of novel sRNAs and indicate an intricate system of gene regulation through sRNAs in A. pleuropneumoniae and in other Pasteurellaceae, thus providing clues for novel aspects of virulence that will be explored in further studies.

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“…1B, second panel) leaving the conserved adenine solvent exposed. 40 However, crystal packing immediately suggested a plausible model for its strict conservation by the formation of RNA-RNA tertiary interactions, which could be subsequently confirmed by all structures including the complete S domain RNA (for human SRP 22,41,42 ). Binding of SRP19 exposes the GNAR adenine for the formation of a non-canonical A-A base pair with the conserved adenine in the classical GNRA-type tetraloop closing helix 8.…”

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confidence: 98%

“…Some of its mysteries could be resolved recently by structure determination of the ternary complex of human SRP68-RBD, S domain RNA and SRP19. 22 The purely a-helical SRP68-RBD has similarity to a tetratricopeptide repeat (TPR) fold (Fig. 1B, third panel).…”

mentioning

confidence: 98%

“…The structure of mammalian SRP has been determined by cryo-EM studies in the context of the ribosomenascent chain complex (RNC), 20,21 but is not available on its own. In the past 15 years, sub-structures of mammalian SRP have been determined, but it was only this year that the mechanism of the Keywords: Ribonucleoprotein complex (RNP), RNA folding, RNA structure, RNP assembly, RNA-RNA tertiary interactions, protein-RNA interactions, signal recognition particle (SRP) S domain remodeling RNA-binding domain of the SRP68 protein was described, 22 which we will now integrate in the current scheme of SRP assembly. SRP RNA is transcribed by RNA polymerase III and is only slightly processed.…”

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confidence: 99%

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RNA gymnastics in mammalian signal recognition particle assembly

Wild

Sinning

2014

RNA Biology

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More than one third of the cellular proteome is destined for incorporation into cell membranes or export from the cell. In all domains of life, the signal recognition particle (SRP) delivers these proteins to the membrane and protein traffic falls apart without SRP logistics. With the aid of a topogenic transport signal, SRP retrieves its cargo right at the ribosome, from where they are sorted to the translocation channel. Mammalian SRP is a ribonucleoprotein complex consisting of an SRP RNA of 300 nucleotides and 6 proteins bound to it. Assembly occurs in a hierarchical manner mainly in the nucleolus and only SRP54, which recognizes the signal sequence and regulates the targeting process, is added as the last component in the cytosol. Here we present an update on recent insights in the structure, function and dynamics of SRP RNA in SRP assembly with focus on the S domain, and present SRP as an example for the complex biogenesis of a rather small ribonucleoprotein particle.

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SRP RNA Remodeling by SRP68 Explains Its Role in Protein Translocation

Cited by 42 publications

References 55 publications

Structures of human SRP72 complexes provide insights into SRP RNA remodeling and ribosome interaction

Structures of human SRP72 complexes provide insights into SRP RNA remodeling and ribosome interaction

A computational strategy for the search of regulatory small RNAs in Actinobacillus pleuropneumoniae

RNA gymnastics in mammalian signal recognition particle assembly

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