Structural Basis for Conserved Regulation and Adaptation of the Signal Recognition Particle Targeting Complex

Wild, Klemens; Bange, Gert; Motiejunas, Domantas; Kribelbauer, Judith F.; Hendricks, Astrid; Segnitz, Bernd; Wade, Rebecca C.; Sinning, Irmgard

doi:10.1016/j.jmb.2016.05.015

Cited by 42 publications

(68 citation statements)

References 56 publications

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“…Our data showing a conserved SRP RNA kink indicate the general conservation of targeting complex activation by RNA. Such mechanism is supported by the conservation of the respective RNA interaction sites in the targeting complexes from all kingdoms of life (6). …”

Section: Resultsmentioning

confidence: 99%

“…Positively-charged surface patches on the targeting complex (6) are readily available to bind to phosphorylated serine residues within the SRP72 tail. As caspase cleavage removes the C-terminal tail, SRP targeting would be clearly impaired.…”

Section: Discussionmentioning

confidence: 99%

“…In eukaryotes, SRP—ribosome nascent chain complexes (RNCs) are targeted to the endoplasmic reticulum by guanosine-5′-triphosphate- (GTP-) dependent interaction with the membrane-bound SRP receptor (SRαβ) and the RNC is transferred to a vacant translocation channel (Sec 61 complex) (2,3). The heterodimeric targeting complex formed by the SRP GTPases SRP54 and SRα constitutes the core of the SRP system and regulates the entire process (4–6). After the RNC is handed over to the translocation channel and translation resumes, the targeting complex relocates on SRP RNA and the SRP GTPases are stimulated by a regulatory ‘distal site’ of the RNA.…”

Section: Introductionmentioning

confidence: 99%

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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: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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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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“…Bacterial complexes of the closed state depicted an NG heterodimer detached from the SRP RNA tetraloop in which the distal region of the SRP RNA could not be fully visualized due to flexibility918. Previous cryo-EM studies on the eukaryotic SRP–SR complex revealed an additional density at the SRP distal region19 that was recently interpreted by docking a crystal structure of the eukaryotic NG heterodimer into this density202122.…”

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confidence: 99%

Structure of the quaternary complex between SRP, SR, and translocon bound to the translating ribosome

Jomaa

Boehringer

et al. 2017

Nat Commun

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During co-translational protein targeting, the signal recognition particle (SRP) binds to the translating ribosome displaying the signal sequence to deliver it to the SRP receptor (SR) on the membrane, where the signal peptide is transferred to the translocon. Using electron cryo-microscopy, we have determined the structure of a quaternary complex of the translating Escherichia coli ribosome, the SRP–SR in the ‘activated' state and the translocon. Our structure, supported by biochemical experiments, reveals that the SRP RNA adopts a kinked and untwisted conformation to allow repositioning of the ‘activated' SRP–SR complex on the ribosome. In addition, we observe the translocon positioned through interactions with the SR in the vicinity of the ribosome exit tunnel where the signal sequence is extending beyond its hydrophobic binding groove of the SRP M domain towards the translocon. Our study provides new insights into the mechanism of signal sequence transfer from the SRP to the translocon.

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“…This protein is part of a ribonucleoprotein complex in which SRP54 forms a heterodimer with the protein FtsY. The crystallographic structure of this heterodimer was solved recently (PDB code: 5L3S) [37]. Alternatively, using the PHYRE2 program, a 22% identity was found between Tc964 and the glycolytic enzyme enolase from Escherichia coli (PDB code: 2FYM) [38].…”

Section: Tc964 Protein May Be a Member Of The Gtpase Familymentioning

confidence: 99%

Molecular Characterization of Tc964, A Novel Antigenic Protein from Trypanosoma cruzi

Ruiz-Márvez

Ramírez

Rodríguez

et al. 2020

IJMS

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The Tc964 protein was initially identified by its presence in the interactome associated with the LYT1 mRNAs, which code for a virulence factor of Trypanosoma cruzi. Tc964 is annotated in the T. cruzi genome as a hypothetical protein. According to phylogenetic analysis, the protein is conserved in the different genera of the Trypanosomatidae family; however, recognizable orthologues were not identified in other groups of organisms. Therefore, as a first step, an in-depth molecular characterization of the Tc946 protein was carried out. Based on structural predictions and molecular dynamics studies, the Tc964 protein would belong to a particular class of GTPases. Subcellular fractionation analysis indicated that Tc964 is a nucleocytoplasmic protein. Additionally, the protein was expressed as a recombinant protein in order to analyze its antigenicity with sera from Chagas disease (CD) patients. Tc964 was found to be antigenic, and B-cell epitopes were mapped by the use of synthetic peptides. In parallel, the Leishmania major homologue (Lm964) was also expressed as recombinant protein and used for a preliminary evaluation of antigen cross-reactivity in CD patients. Interestingly, Tc964 was recognized by sera from Chronic CD (CCD) patients at different stages of disease severity, but no reactivity against this protein was observed when sera from Colombian patients with cutaneous leishmaniasis were analyzed. Therefore, Tc964 would be adequate for CD diagnosis in areas where both infections (CD and leishmaniasis) coexist, even though additional assays using larger collections of sera are needed in order to confirm its usefulness for differential serodiagnosis.

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Structural Basis for Conserved Regulation and Adaptation of the Signal Recognition Particle Targeting Complex

Cited by 42 publications

References 56 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

Structure of the quaternary complex between SRP, SR, and translocon bound to the translating ribosome

Molecular Characterization of Tc964, A Novel Antigenic Protein from Trypanosoma cruzi

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