Proteotoxic stress promotes entrapment of ribosomes and misfolded proteins in a shared cytosolic compartment.

Abstract:

:Cells continuously monitor protein synthesis to prevent accumulation of aberrant polypeptides. Insufficient capacity of cellular degradative systems, chaperone shortage or high levels of mistranslation by ribosomes can result in proteotoxic stress and endanger proteostasis. One of the least explored reasons for mistranslation is the incorrect functioning of the ribosome itself. To understand how cells deal with ribosome malfunction, we introduced mutations in the Expansion Segment 7 (ES7L) of 25S rRNA that allowed the formation of mature, translationally active ribosomes but induced proteotoxic stress and compromised cell viability. The ES7L-mutated ribosomes escaped nonfunctional rRNA Decay (NRD) and remained stable. Remarkably, ES7L-mutated ribosomes showed increased segregation into cytoplasmic foci containing soluble misfolded proteins. This ribosome entrapment pathway, termed TRAP (Translational Relocalization with Aberrant Polypeptides), was generalizable beyond the ES7L mutation, as wild-type ribosomes also showed increased relocalization into the same compartments in cells exposed to proteotoxic stressors. We propose that during TRAP, assembled ribosomes associated with misfolded nascent chains move into cytoplasmic compartments enriched in factors that facilitate protein quality control. In addition, TRAP may help to keep translation at its peak efficiency by preventing malfunctioning ribosomes from active duty in translation.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Ghosh A,Williams LD,Pestov DG,Shcherbik N

doi

10.1093/nar/gkaa068

subject

Has Abstract

pub_date

2020-04-17 00:00:00

pages

3888-3905

issue

7

eissn

0305-1048

issn

1362-4962

pii

5728877

journal_volume

48

pub_type

杂志文章
  • Analysis of the gene encoding the RNA subunit of ribonuclease P from cyanobacteria.

    abstract::The genes encoding the RNA subunit of ribonuclease P from the unicellular cyanobacterium Synechocystis sp. PCC 6803, and from the heterocyst-forming strains Anabaena sp. PCC 7120 and Calothrix sp. PCC 7601 were cloned using the homologous gene from Anacystis nidulans (Synechococcus sp. PCC 6301) as a probe. The genes ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/20.23.6331

    authors: Vioque A

    更新日期:1992-12-11 00:00:00

  • Bacillus cereus DNA topoisomerase I and IIIalpha: purification, characterization and complementation of Escherichia coli TopoIII activity.

    abstract::The Bacillus cereus genome possesses three type IA topoisomerase genes. These genes, encoding DNA topoisomerase I and IIIalpha (bcTopo I, bcTopo IIIalpha), have been cloned into T7 RNA polymerase-regulated plasmid expression vectors and the enzymes have been overexpressed, purified and characterized. The proteins exhi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gki846

    authors: Li Z,Hiasa H,DiGate R

    更新日期:2005-09-28 00:00:00

  • Comparison of approaches for rational siRNA design leading to a new efficient and transparent method.

    abstract::Current literature describes several methods for the design of efficient siRNAs with 19 perfectly matched base pairs and 2 nt overhangs. Using four independent databases totaling 3336 experimentally verified siRNAs, we compared how well several of these methods predict siRNA cleavage efficiency. According to receiver ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkm088

    authors: Matveeva O,Nechipurenko Y,Rossi L,Moore B,Saetrom P,Ogurtsov AY,Atkins JF,Shabalina SA

    更新日期:2007-01-01 00:00:00

  • Two promoter elements are necessary and sufficient for expression of the sea urchin U1 snRNA gene.

    abstract::The essential elements of the sea urchin L. variegatus U1 snRNA promoter were mapped by microinjection of a U1 maxigene into sea urchin zygotes. Two elements are required for expression: a distal sequence element (DSE) located between -318 and -300 and a proximal sequence element (PSE) centered at -55. Removal or alte...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/20.14.3743

    authors: Wendelburg BJ,Marzluff WF

    更新日期:1992-07-25 00:00:00

  • The isolation of a human Ig V lambda gene from a recombinant library of chromosome 22 and estimation of its copy number.

    abstract::We report the first isolation and characterisation of a human Ig V lambda gene. The gene was isolated from a recombinant phage library of human chromosome 22 using a mouse Ig lambda cDNA as probe. DNA sequence analysis predicts a short leader peptide interrupted by an intron of 88 nucleotides, and a mature polypeptide...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/12.17.6647

    authors: Anderson ML,Szajnert MF,Kaplan JC,McColl L,Young BD

    更新日期:1984-09-11 00:00:00

  • Alternative pathways for editing non-cognate amino acids by aminoacyl-tRNA synthetases.

    abstract::Evidence is presented that the editing mechanisms of aminoacyl-tRNA synthetase operate by two alternative pathways: pre-transfer, by hydrolysis of the non-cognate aminoacyl adenylate; post-transfer, by hydrolysis of the mischarged tRNA. The methionyl-tRNA synthetases from Escherichia coli and Bacillus stearothermophil...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/9.13.3105

    authors: Jakubowski H,Fersht AR

    更新日期:1981-07-10 00:00:00

  • Dual roles of yeast Rad51 N-terminal domain in repairing DNA double-strand breaks.

    abstract::Highly toxic DNA double-strand breaks (DSBs) readily trigger the DNA damage response (DDR) in cells, which delays cell cycle progression to ensure proper DSB repair. In Saccharomyces cerevisiae, mitotic S phase (20-30 min) is lengthened upon DNA damage. During meiosis, Spo11-induced DSB onset and repair lasts up to 5 ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkaa587

    authors: Woo TT,Chuang CN,Higashide M,Shinohara A,Wang TF

    更新日期:2020-09-04 00:00:00

  • Sequencing of an upstream region of the human HLA-DRA gene containing X' and Y' boxes.

    abstract::In this paper we report the characterization of a newly sequenced 5' upstream region of the human HLA-DRA gene. We performed (i) search for transcription factor motifs, (ii) analysis of CpG display and observed/expected frequency ratios, (iii) search for regions homologous to the 5' upstream sequences of the murine EA...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/23.10.1671

    authors: Feriotto G,Mischiati C,Bianchi N,Rutigliano C,Giacomini P,Gambari R

    更新日期:1995-05-25 00:00:00

  • Pausing of reverse transcriptase on retroviral RNA templates is influenced by secondary structures both 5' and 3' of the catalytic site.

    abstract::In the most extensive examination to date of the relationship between the pausing of reverse transcrip-tase (RT) and RNA secondary structures, pause events were found to be correlated to inverted repeats both ahead of, and behind the catalytic site in vitro. In addition pausing events were strongly associated with pol...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/26.14.3433

    authors: Harrison GP,Mayo MS,Hunter E,Lever AM

    更新日期:1998-07-15 00:00:00

  • Phosphoramidate analogues of DNA: synthesis and thermal stability of heteroduplexes.

    abstract::The deoxyoligonucleotide 5' AATCGGGCATGGATT (15-mer) was synthesized containing 12 phosphoramidate linkages derived from 2 primary and 2 secondary amines. The oligonucleotides were purified by reverse phase HPLC and characterized by PAGE. The thermal stability of the duplexes derived from these compounds, when hybridi...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/16.11.4831

    authors: Froehler B,Ng P,Matteucci M

    更新日期:1988-06-10 00:00:00

  • GOBASE: an organelle genome database.

    abstract::The organelle genome database GOBASE, now in its 21st release (June 2008), contains all published mitochondrion-encoded sequences (approximately 913,000) and chloroplast-encoded sequences (approximately 250,000) from a wide range of eukaryotic taxa. For all sequences, information on related genes, exons, introns, gene...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkn819

    authors: O'Brien EA,Zhang Y,Wang E,Marie V,Badejoko W,Lang BF,Burger G

    更新日期:2009-01-01 00:00:00

  • The human Obg protein GTPBP10 is involved in mitoribosomal biogenesis.

    abstract::The human mitochondrial translation apparatus, which synthesizes the core subunits of the oxidative phosphorylation system, is of central interest as mutations in several genes encoding for mitoribosomal proteins or translation factors cause severe human diseases. Little is known, how this complex machinery assembles ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gky701

    authors: Lavdovskaia E,Kolander E,Steube E,Mai MM,Urlaub H,Richter-Dennerlein R

    更新日期:2018-09-19 00:00:00

  • Structure of the hypusinylated eukaryotic translation factor eIF-5A bound to the ribosome.

    abstract::During protein synthesis, ribosomes become stalled on polyproline-containing sequences, unless they are rescued in archaea and eukaryotes by the initiation factor 5A (a/eIF-5A) and in bacteria by the homologous protein EF-P. While a structure of EF-P bound to the 70S ribosome exists, structural insight into eIF-5A on ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkv1517

    authors: Schmidt C,Becker T,Heuer A,Braunger K,Shanmuganathan V,Pech M,Berninghausen O,Wilson DN,Beckmann R

    更新日期:2016-02-29 00:00:00

  • Localisation of the human hSuv3p helicase in the mitochondrial matrix and its preferential unwinding of dsDNA.

    abstract::We characterised the human hSuv3p protein belonging to the family of NTPases/helicases. In yeast mitochondria the hSUV3 orthologue is a component of the degradosome complex and participates in mtRNA turnover and processing, while in Caenorhabditis elegans the hSUV3 orthologue is necessary for viability of early embryo...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkf647

    authors: Minczuk M,Piwowarski J,Papworth MA,Awiszus K,Schalinski S,Dziembowski A,Dmochowska A,Bartnik E,Tokatlidis K,Stepien PP,Borowski P

    更新日期:2002-12-01 00:00:00

  • MAGNET: MicroArray Gene expression and Network Evaluation Toolkit.

    abstract::MicroArray Gene expression and Network Evaluation Toolkit (MAGNET) is a web-based application that provides tools to generate and score both protein-protein interaction networks and coexpression networks. MAGNET integrates user-provided experimental measurements with high-throughput proteomic datasets, generating weig...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks526

    authors: Linderman GC,Chance MR,Bebek G

    更新日期:2012-07-01 00:00:00

  • Apple II software for M13 shotgun DNA sequencing.

    abstract::A set of programs is presented for the reconstruction of a DNA sequence from data generated by the M13 shotgun sequencing technique. Once the sequence has been established and stored other programs are used for its analysis. The programs have been written for the Apple II microcomputer. A minimum investment is require...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/10.1.39

    authors: Larson R,Messing J

    更新日期:1982-01-11 00:00:00

  • Influence of ground-state structure and Mg2+ binding on folding kinetics of the guanine-sensing riboswitch aptamer domain.

    abstract::Riboswitch RNAs fold into complex tertiary structures upon binding to their cognate ligand. Ligand recognition is accomplished by key residues in the binding pocket. In addition, it often crucially depends on the stability of peripheral structural elements. The ligand-bound complex of the guanine-sensing riboswitch fr...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkr664

    authors: Buck J,Wacker A,Warkentin E,Wöhnert J,Wirmer-Bartoschek J,Schwalbe H

    更新日期:2011-12-01 00:00:00

  • Spectroscopic studies of (m5dC-dG)3: thermal stability of B- and Z-forms.

    abstract::The hexanucleoside pentaphosphate d(m5CpGpm5CpGpm5CpG) has been studied in solution by ultra-violet absorption, circular dichroism and 31P nuclear magnetic resonance under various experimental conditions. In 0.2 M NaClO4 at low temperature, an hexamer duplex is formed which has a B or B-like conformation. As the salt ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/11.13.4453

    authors: Hartmann B,Thuong NT,Pouyet J,Ptak M,Leng M

    更新日期:1983-07-11 00:00:00

  • Persistence of DNA synthesis arrest sites in the presence of T4 DNA polymerase and T4 gene 32, 44, 45 and 62 DNA polymerase accessory proteins.

    abstract::DNA synthesis by phage T4 DNA polymerase is arrested at specific sequences in single-stranded DNA templates. To determine whether or not T4 DNA polymerase accessory proteins 32, 44, 45 and 62 eliminated recognition of these arrest sites, unique primer-templates were constructed in which DNA synthesis began at a DNA pr...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/14.8.3343

    authors: Charette MF,Weaver DT,DePamphilis ML

    更新日期:1986-04-25 00:00:00

  • Cell cycle regulated synthesis of an abundant transcript for human chromosomal protein HMG-17.

    abstract::The abundance and cell cycle dependent expression of the mRNA for human nonhistone protein HMG-17 were studied in synchronized HeLa cells. Slot blot analysis indicates that the HMG-17 mRNA is a very abundant message, significantly more so than histone or actin mRNA. RNA prepared from tissue culture cells contains high...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/15.8.3549

    authors: Bustin M,Soares N,Landsman D,Srikantha T,Collins JM

    更新日期:1987-04-24 00:00:00

  • An error-prone family Y DNA polymerase (DinB homolog from Sulfolobus solfataricus) uses a 'steric gate' residue for discrimination against ribonucleotides.

    abstract::DNA polymerases of the A and B families, and reverse transcriptases, share a common mechanism for preventing incorporation of ribonucleotides: a highly conserved active site residue obstructing the position that would be occupied by a 2' hydroxyl group on the incoming nucleotide. In the family Y (lesion bypass) polyme...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkg417

    authors: DeLucia AM,Grindley ND,Joyce CM

    更新日期:2003-07-15 00:00:00

  • Comparative sequence and structure of viroid-like RNAs of two plant viruses.

    abstract::A newly discovered group of spherical plant viruses contains a bipartite genome consisting of a single-strand linear RNA molecule (RNA 1, Mr 1.5 x 10(6) ), and a single-strand, covalently closed circular viroid-like RNA molecule (RNA 2, Mr approximately 125,000). The nucleotide sequences of the RNA 2 of two of these, ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/10.12.3681

    authors: Haseloff J,Symons RH

    更新日期:1982-06-25 00:00:00

  • The repeating nucleotide sequence in the repetitive mitochondrial DNA from a "low-density" petite mutant of yeast.

    abstract::The repeating nucleotide sequence of 68 base pairs in the mtDNA from an ethidium-induced cytoplasmic petite mutant of yeast has been determined. For sequence analysis specifically primed and terminated RNA copies, obtained by in vitro transcription of the separated strands, were use. The sequence consists of 66 consec...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/4.7.2369

    authors: Van Kreijl CF,Bos JL

    更新日期:1977-07-01 00:00:00

  • A novel endonuclease IV post-PCR genotyping system.

    abstract::Here we describe a novel endonuclease IV (Endo IV) based assay utilizing a substrate that mimics the abasic lesions that normally occur in double-stranded DNA. The three component substrate is characterized by single-stranded DNA target, an oligonucleotide probe, separated from a helper oligonucleotide by a one base g...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl679

    authors: Kutyavin IV,Milesi D,Belousov Y,Podyminogin M,Vorobiev A,Gorn V,Lukhtanov EA,Vermeulen NM,Mahoney W

    更新日期:2006-01-01 00:00:00

  • OMA 2011: orthology inference among 1000 complete genomes.

    abstract::OMA (Orthologous MAtrix) is a database that identifies orthologs among publicly available, complete genomes. Initiated in 2004, the project is at its 11th release. It now includes 1000 genomes, making it one of the largest resources of its kind. Here, we describe recent developments in terms of species covered; the al...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkq1238

    authors: Altenhoff AM,Schneider A,Gonnet GH,Dessimoz C

    更新日期:2011-01-01 00:00:00

  • Unique sequences are interspersed among tandemly repeated elements in the murine gamma 1 switch segment.

    abstract::Early in its differentiative pathway, a given B lymphocyte expresses immunoglobulin of the mu heavy chain class (IgM). Subsequent differentiative processes may involve rearrangement within the immunoglobulin heavy chain chromosomal locus to enable cells of the same lineage to synthesize immunoglobulins of other heavy ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/13.1.225

    authors: Mowatt M,Dery C,Dunnick W

    更新日期:1985-01-11 00:00:00

  • RB signaling prevents replication-dependent DNA double-strand breaks following genotoxic insult.

    abstract::Cell cycle checkpoints induced by DNA damage play an integral role in preservation of genomic stability by allowing cells to limit the propagation of deleterious mutations. The retinoblastoma tumor suppressor (RB) is crucial for the maintenance of the DNA damage checkpoint function because it elicits cell cycle arrest...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkg919

    authors: Bosco EE,Mayhew CN,Hennigan RF,Sage J,Jacks T,Knudsen ES

    更新日期:2004-01-02 00:00:00

  • Gene delivery by dendrimers operates via a cholesterol dependent pathway.

    abstract::Understanding the cellular uptake and intracellular trafficking of dendrimer-DNA complexes is an important prerequisite for improving the transfection efficiency of non-viral vector-mediated gene delivery. Dendrimers are synthetic polymers used for gene transfer. Although these cationic molecules show promise as versa...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkh595

    authors: Manunta M,Tan PH,Sagoo P,Kashefi K,George AJ

    更新日期:2004-05-17 00:00:00

  • The inhibition of mitochondrial DNA polymerase gamma from animal cells by intercalating drugs.

    abstract::DNA polymerase gamma from purified nuclei of EMT-6 cells (mice) seems to be identical to the mitochondrial DNA polymerase from the same source following several criteria. These two enzyme activities are strongly inhibited by ethidium bromide and acriflavin, while proflavin, acridine orange, daunomycin and chloroquine ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/5.6.2197

    authors: Tarrago-Litvak L,Viratelle O,Darriet D,Dalibart R,Graves PV,Litvak S

    更新日期:1978-06-01 00:00:00

  • Elongation complexes of Thermus thermophilus RNA polymerase that possess distinct translocation conformations.

    abstract::We have characterized elongation complexes (ECs) of RNA polymerase from the extremely thermophilic bacterium, Thermus thermophilus. We found that complexes assembled on nucleic acid scaffolds are transcriptionally competent at high temperature (50-80 degrees C) and, depending upon the organization of the scaffold, pos...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl559

    authors: Kashkina E,Anikin M,Tahirov TH,Kochetkov SN,Vassylyev DG,Temiakov D

    更新日期:2006-01-01 00:00:00