Implications of the SRP72 p.R124S mutation on signal recognition particle functions [K562_SRP72]
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA923605 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23073292_1.fastq.gz | Fastqsanger.gz | |||
| SRR23073292_2.fastq.gz | Fastqsanger.gz | |||
| SRR23073293_1.fastq.gz | Fastqsanger.gz | |||
| SRR23073293_2.fastq.gz | Fastqsanger.gz | |||
| SRR23073294_1.fastq.gz | Fastqsanger.gz |
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Project description:To investigate the functional significance of the SRP72 p.R124S mutation, we overexpressed the mutant protein in K562 myeloid leukemia cells and analysed global gene expression changes using RNA-seq.
2023-05-02 | GSE222812 | GEO
Project description:Decoding the Significance of Amino Acid-dependent Signal Recognition Particle 9 Nuclear Translocation: Implications for Pancreatic Cancer Prognosis and Functionality [RIP-seq]
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Project description:Signal recognition particles (SRPs) are important components in regulating intracellular protein transport and secretion, and tumors with high expression of Signal recognition particle 9 (SRP9) have tended to have poorer overall survival, although no reports have described the relationship between its localization and prognosis in pancreatic cancer. We conducted immunohistochemical staining for SRP9 for excised specimens from pancreatic cancer surgery cases without preoperative chemotherapy or radiotherapy performed. We found that in some cases SRP9 was preferentially expressed in the nucleus of the cancerous regions, which was hardly detected in other cases, suggesting SRP9 was transported to nucleus in the former cases. Therefore, the prognosis of patients with SRP9 nuclear translocation was compared by dividing them into two groups: those with a nuclear translocation rate of >50% and ≤50%. Patients with a nuclear translocation rate of >50% had significantly better recurrence-free survival compared with nuclear translocation rate of ≤50% group (p = 0.037). Subsequent in vitro experiments also showed that its nuclear translocation rate is reduced under amino acid deficient conditions. Further, to investigate the mechanism of SRP9 nuclear translocation, we studied in vitro by introducing the genes of SRP9 splicing variants (v1 and v2) and their deletion mutants lacking C-terminal regions into MiaPaCa pancreatic cancer cells. As a result, it was confirmed that both splicing variants showed nuclear translocation regardless of C-terminal deletions. Taking advantage of the fact that SRP9 is an RNA-binding protein, we next decided to sequence RNAs that bind to nuclear translocated v1 and v2 and evaluate their function in nuclear translocation. RNA Immunoprecipitation Sequencing of nuclear translocated v1 and v2 showed that pathways involved in cancer progression and protein translation were downregulated. The further study of nuclear translocation of SRP9 may open an avenue to optimization of precise evaluation and therapeutic control of pancreatic cancer.
2024-01-12 | GSE246628 | GEO
Project description:The proper functioning of many proteins requires their transport to the correct cellular compartment or their secretion. Signal recognition particle (SRP) is a major protein transport pathway responsible for the co-translational movement of integral membrane proteins as well as periplasmic proteins. Deinococcus radiodurans is a ubiquitous bacterium that expresses a complex phenotype of extreme oxidative stress resistance, which is mediated by proteins involved in DNA repair, metabolism, gene regulation and antioxidant defence. These proteins are located either extracellularly or subcellularly, but the molecular mechanism of protein localization in D. radiodurans to manage oxidative stress response remains unexplored. In this study, we characterized the SRP complex in D. radiodurans R1 and showed that the knockdown of the SRP RNA (Qpr6) reduced bacterial survival under hydrogen peroxide (H2O2) and growth under chronic ionizing radiation (CIR). Through LC-MS/MS analysis, we detected 162 proteins in the periplasm of wild-type D. radiodurans, of which the transport of 65 of these proteins to the periplasm was significantly reduced in the Qpr6 knockdown strain. Through Western blotting, we further demonstrated the localization of the catalases in D. radiodurans, DR_1998 (KatE1) and DR_A0259 (KatE2), in both the cytoplasm and periplasm, and showed that the accumulation of KatE1 and KatE2 in the periplasm was reduced in the SRP-defective (Qpr6 knockdown) strain.
2023-03-11 | PXD022570 | Pride
Project description:The signal-recognition particle (SRP) is a ubiquitous protein-RNA complex that targets proteins to cellular membranes for insertion or secretion. A key player in SRP-mediated protein targeting is the evolutionarily conserved core consisting of the SRP RNA and the multidomain protein SRP54. Communication between the SRP54 domains is critical for SRP function, where signal sequence binding at the M domain directs receptor binding at the GTPase domain (NG domain). These SRP activities are linked to domain rearrangements, for which the role of SRP RNA is not clear. In free SRP, a direct interaction of the GTPase domain with SRP RNA has been proposed but has never been structurally verified. In this study, we present the crystal structure at 2.5-A resolution of the SRP54-SRP19-SRP RNA complex of Methanococcus jannaschii SRP. The structure reveals an RNA-bound conformation of the SRP54 GTPase domain, in which the domain is spatially well separated from the signal peptide binding site. The association of both the N and G domains with SRP RNA in free SRP provides further structural evidence for the pivotal role of SRP RNA in the regulation of the SRP54 activity.
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Project description:The signal recognition particle (SRP) is a ribonucleoprotein complex fundamental for co-translational delivery of proteins to their proper membrane localization and secretory pathways. Literature of the past two decades has suggested new roles for individual SRP components, 7SL RNA and proteins SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72, outside the SRP cycle. These noncanonical functions interconnect SRP with a multitude of cellular and molecular pathways, including virus-host interactions, stress response, transcriptional regulation and modulation of apoptosis in autoimmune diseases. Uncovered novel properties of the SRP components present a new perspective for the mammalian SRP as a biological modulator of multiple cellular processes. As a consequence of these findings, SRP components have been correlated with a growing list of diseases, such as cancer progression, myopathies and bone marrow genetic diseases, suggesting a potential for development of SRP-target therapies of each individual component. For the first time, here we present the current knowledge on the SRP noncanonical functions and raise the need of a deeper understanding of the molecular interactions between SRP and accessory cellular components. We examine diseases associated with SRP components and discuss the development and feasibility of therapeutics targeting individual SRP noncanonical functions.
| S-EPMC8185352 | biostudies-literature
Project description:Targeting of proteins to appropriate subcellular compartments is a crucial process in all living cells. Secretory and membrane proteins usually contain an amino-terminal signal peptide, which is recognized by the signal recognition particle (SRP) when nascent polypeptide chains emerge from the ribosome. The SRP-ribosome nascent chain complex is then targeted through its GTP-dependent interaction with SRP receptor to the protein-conducting channel on endoplasmic reticulum membrane in eukaryotes or plasma membrane in bacteria. A universally conserved component of SRP (refs 1, 2), SRP54 or its bacterial homologue, fifty-four homologue (Ffh), binds the signal peptides, which have a highly divergent sequence divisible into a positively charged n-region, an h-region commonly containing 8-20 hydrophobic residues and a polar c-region. No structure has been reported that exemplifies SRP54 binding of any signal sequence. Here we have produced a fusion protein between Sulfolobus solfataricus SRP54 (Ffh) and a signal peptide connected via a flexible linker. This fusion protein oligomerizes in solution through interaction between the SRP54 and signal peptide moieties belonging to different chains, and it is functional, as demonstrated by its ability to bind SRP RNA and SRP receptor FtsY. We present the crystal structure at 3.5 A resolution of an SRP54-signal peptide complex in the dimer, which reveals how a signal sequence is recognized by SRP54.
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Project description:The signal recognition particle database (SRPDB) is maintained at the University of Texas Health Science Center at Tyler, Texas, and organizes SRP-related information about SRP RNA, SRP proteins and the SRP receptor. SRPDB is accessible on the WWW at the URL http://psyche.uthct.edu/dbs/SRPDB/SRPDB.++ +html. A mirror site of the SRPDB is located in Europe at the University of Göteborg, Sweden (http://www.medkem. gu.se/dbs/SRPDB/SRPDB.html ). This release of SRPDB adds 10 new SRP RNA sequences (a total of 117 SRP RNAs), four protein SRP19 sequences (a total of 15), seven new SRP54 (ffh) sequences (a total of 52), and eight sequences of the SRP receptor alpha subunit (FtsY) (total of 36). Sequences are arranged in alphabetical and phylogenetic order and alignments are provided which highlight base paired and conserved regions. SPRDB also provides motifs to find new sequences, a brief introduction to SRP function in protein secretion, numerous SRP RNA secondary structure diagrams, 3-D SRP RNA models, and recently obtained crystal structure PDB coordinates of the human SRP54m domain.
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Project description:The signal recognition particle (SRP) is a ribonucleoprotein complex with dual functions. It co-translationally targets proteins with a signal sequence to the endoplasmic reticulum (ER) and protects their mRNA from degradation. If SRP is depleted or cannot recognize the signal sequence, then the Regulation of Aberrant Protein Production (RAPP) is activated, which results in the loss of secretory protein mRNA. If SRP recognizes the substrates but is unable to target them to ER, they may mislocalize or degrade. All these events lead to dramatic consequence for protein biogenesis, activating protein quality control pathways, and creating pressure on cell physiology, and might lead to the pathogenesis of disease. Indeed, SRP dysfunction is involved in many different human diseases, including: congenital neutropenia; idiopathic inflammatory myopathy; viral, protozoal, and prion infections; and cancer. In this work, we analyze diseases caused by SRP failure and discuss their possible molecular mechanisms.
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