Translation is an emerging constraint on protein homeostasis in ageing

Trends in Cell Biology, Journal Year: 2024, Volume and Issue: 34(8), P. 646 - 656

Published: Feb. 28, 2024

Proteins are molecular machines that provide structure and perform vital transport, signalling enzymatic roles. expressed by cells require tight regulation of their concentration, folding, localisation, modifications; however, this state protein homeostasis is continuously perturbed tissue-level stresses. While in healthy tissues able to buffer against these perturbations, for example, expression chaperone proteins, lost ageing, can lead aggregation characteristic folding diseases. Here, we review reports a progressive disconnect between transcriptomic proteomic during cellular ageing. We discuss how age-associated changes responses specific stressors the tissue microenvironment exacerbated loss ribosomal pausing, mistranslation.

Language: Английский

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A role for the S4-domain containing protein YlmH in ribosome-associated quality control in Bacillus subtilis

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: 52(14), P. 8483 - 8499

Published: May 30, 2024

Ribosomes trapped on mRNAs during protein synthesis need to be rescued for the cell survive. The most ubiquitous bacterial ribosome rescue pathway is trans-translation mediated by tmRNA and SmpB. Genetic inactivation of can lethal, unless ribosomes are ArfA or ArfB alternative factors ribosome-associated quality control (RQC) system, which in Bacillus subtilis involves MutS2, RqcH, RqcP Pth. Using transposon sequencing a trans-translation-incompetent B. strain we identify poorly characterized S4-domain-containing YlmH as novel potential RQC factor. Cryo-EM structures reveal that binds peptidyl-tRNA-50S complexes position analogous RqcP, that, similarly co-habit with RqcH. Consistently, show assume role facilitating addition poly-alanine tails truncated nascent polypeptides. While function redundant our taxonomic analysis reveals multiple phyla absent, while RqcH present, suggesting these species plays central RQC.

Language: Английский

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Stalled disomes marked by Hel2-dependent ubiquitin chains undergo Ubp2/Ubp3-mediated deubiquitination upon translational run-off

Communications Biology, Journal Year: 2025, Volume and Issue: 8(1)

Published: Jan. 28, 2025

Abstract Stalled ribosomes cause collisions, impair protein synthesis, and generate potentially harmful truncated polypeptides. Eukaryotic cells utilize the ribosome-associated quality control (RQC) no-go mRNA decay (NGD) pathways to resolve these problems. In yeast, E3 ubiquitin ligase Hel2 recognizes polyubiquitinates disomes trisomes at 40S ribosomal Rps20/uS10, thereby priming for further steps in RQC/NGD pathways. Recent studies have revealed high concentrations of unstressed cells, raising question whether how selects long-term stalled trisomes. This study presents quantitative analysis vivo-formed Hel2•ribosome complexes dynamics Hel2-dependent Rps20 ubiquitination Ubp2/Ubp3-dependent deubiquitination. Our findings show that occupancy progressively increases from translating monosomes We demonstrate with mono- or di-ubiquitinated independently RQC component Slh1, while those tri- tetra-ubiquitinated do not. Based on results, we propose a model which translates duration ribosome stalling into polyubiquitin chain length. mechanism allows distinction between transient stalling, providing machinery means select fatally over transiently ones.

Language: Английский

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Comprehensive translational profiling and STE AI uncover rapid control of protein biosynthesis during cell stress

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: 52(13), P. 7925 - 7946

Published: May 9, 2024

Abstract Translational control is important in all life, but it remains a challenge to accurately quantify. When ribosomes translate messenger (m)RNA into proteins, they attach the mRNA series, forming poly(ribo)somes, and can co-localize. Here, we computationally model new types of co-localized ribosomal complexes on identify them using enhanced translation complex profile sequencing (eTCP-seq) based rapid vivo crosslinking. We detect long disome footprints outside regions non-random elongation stalls show these are linked initiation protein biosynthesis rates. subject disomes other artificial intelligence (AI) analysis construct new, accurate self-normalized measure translation, termed stochastic efficiency (STE). then apply STE investigate changes yeast undergoing glucose depletion. Importantly, that, well beyond tagging stalls, provide rich insight translational mechanisms, polysome dynamics topology. AI ranks cellular mRNAs by absolute rates under given conditions, assist identifying its elements will facilitate development next-generation synthetic biology designs mRNA-based therapeutics.

Language: Английский

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Transcriptional profile of ribosome-associated quality control components and their associated phenotypes in mammalian cells

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: Jan. 16, 2024

Abstract During protein synthesis, organisms detect translation defects that induce ribosome stalling and result in aggregation. The Ribosome-associated Quality Control (RQC) complex, comprising TCF25, LTN1, NEMF, is responsible for identifying incomplete products from unproductive events, targeting them degradation. Although RQC disruption causes adverse effects on vertebrate neurons, data regarding mRNA/protein expression regulation across tissues are lacking. Employing high-throughput methods, we analyzed public datasets to explore gene phenotypes. Our findings revealed widespread of components human tissues; however, silencing yielded only mild negative cell growth. Notably, TCF25 exhibited elevated mRNA levels were not reflected the content. We experimentally demonstrated this disparity arose post-translational degradation by proteasome. Additionally, observed cellular aging marginally influenced expression, leading reduced specific tissues. results suggest necessity all mammalian Nevertheless, when falters, alternative mechanisms seem compensate, ensuring survival under nonstress conditions.

Language: Английский

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Context specific ubiquitin modification of ribosomes regulates translation under oxidative stress

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 3, 2024

ABSTRACT Cellular exposure to stress is known activate several translational control pathways through ribosome ubiquitination. However, how unique patterns of ubiquitination act at the site-specific level drive distinct modes translation regulation remains unclear. To further understand complexity these ubiquitin signals, we developed a new targeted proteomics approach quantify modification across ribosome. This method increased sensitivity and throughput current approaches allowed us systematically measure status 78 peptides linkages in response stress. Using this method, were able detect sites even steady-state conditions, show that their increases non-stoichiometrically dynamic range >4 orders magnitude hydrogen peroxide. Besides demonstrating global ubiquitination, our study also revealed an unexpected increase ribosomal protein uS10/Rps20 uS3/Rps3 independent canonical E3 ligase Hel2. Furthermore, mixed occur specific manner, depending on nature stressor enzymes involved. Finally, showed while deletion HEL2 induces integrated nucleotide alkylating agent 4-NQO, E2 conjugase RAD6 leads sustained only H 2 O . Our findings contribute deciphering level, revealing induction selective codes, which shed light integration important quality during cellular

Language: Английский

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E3 ubiquitin ligase RNF10 promotes dissociation of stalled ribosomes and responds to ribosomal subunit imbalance

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Nov. 28, 2024

Aberrant translation causes ribosome stalling, which leads to the ubiquitination of ribosomal proteins and induces ribosome-associated quality control. As part this control process, E3 ubiquitin ligase RNF10 monoubiquitinates protein RPS3. Here, we demonstrate that RNF10-mediated RPS3 monoubiquitination antagonizes half-mer formation by promoting dissociation 40S subunits from ribosomes stalled during elongation. Interestingly, also promotes aberrant initiation. Moreover, levels are tightly coupled amount subunits. Knockdown RPS proteins, abrogates biogenesis, results in proteasomal degradation RNF10. Vice versa, knockdown RPL 60S accumulation initiating subunits, increased levels, monoubiquitination. a factor required for resolution events, is fundamental mechanism cells respond imbalances subunit stoichiometry.

Language: Английский

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A role for the S4-domain containing protein YlmH in ribosome-associated quality control inBacillus subtilis

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: March 4, 2024

Abstract Ribosomes trapped on mRNAs during protein synthesis need to be rescued for the cell survive. The most ubiquitous bacterial ribosome rescue pathway is trans-translation mediated by tmRNA and SmpB. Genetic inactivation of can lethal, unless ribosomes are ArfA or ArfB alternative factors ribosome-associated quality control (RQC) system, which in B. subtilis involves MutS2, RqcH, RqcP Pth. Using transposon sequencing a trans-translation-incompetent strain we identify poorly characterized S4-domain-containing YlmH as novel potential RQC factor. Cryo-EM structures reveal that binds peptidyl-tRNA-50S complexes an position analogous RqcP, that, similarly co-habit with RqcH. Consistently, show assume role facilitating addition polyalanine tails truncated nascent polypeptides. While function redundant our taxonomic analysis reveals multiple phyla absent, while RqcH present, suggesting these species plays central RQC.

Language: Английский

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Evidence that Xrn1 is in complex with Gcn1, and is required for full levels of eIF2α phosphorylation.

Biochemical Journal, Journal Year: 2024, Volume and Issue: 481(7), P. 481 - 498

Published: March 5, 2024

The protein kinase Gcn2 and its effector Gcn1 are part of the general amino acid control signalling (GAAC) pathway best known in yeast for function maintaining homeostasis. Under limitation, becomes activated, subsequently increasing levels phosphorylated eIF2α (eIF2α-P). This leads to increased translation transcriptional regulators, such as Gcn4 ATF4 mammals, subsequent re-programming cell's gene transcription profile, thereby allowing cells cope with starvation. Xrn1 is involved RNA decay, quality processing. We found that co-precipitates Gcn2, suggesting these three proteins same complex. Growth under starvation conditions was dependent on but not Xrn1-ribosome association, this correlated reduced eIF2α-P levels. Constitutively active a growth defect due eIF2α-hyperphosphorylation, we phenotype independent Xrn1, xrn1 deletion does enhance de-phosphorylation. Our study provides evidence required efficient activation, directly or indirectly. Thus, have uncovered potential new link between metabolism GAAC.

Language: Английский

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The Beak of Eukaryotic Ribosomes: Life, Work and Miracles

Biomolecules, Journal Year: 2024, Volume and Issue: 14(7), P. 882 - 882

Published: July 22, 2024

Ribosomes are not totally globular machines. Instead, they comprise prominent structural protrusions and a myriad of tentacle-like projections, which frequently made up ribosomal RNA expansion segments N- or C-terminal extensions proteins. This is more evident in higher eukaryotic ribosomes. One the most characteristic protrusions, present small subunits all three domains life, so-called beak, relevant for function regulation ribosome’s activities. During evolution, beak has transitioned from an structure (helix h33 16S rRNA) bacteria, to arrangement formed by proteins, eS10, eS12 eS31, smaller eukaryotes. In this review, we describe different functional properties beak. We discuss state-of-the-art concerning its composition significance, including other processes apparently related translation, dynamics assembly yeast human cells. Moreover, outline current view about relevance beak’s components diseases, especially ribosomopathies cancer.

Language: Английский

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