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Mapping translation initiation sites by ribosome profiling in primary mouse cortical neurons treated with either DMSO or bicuculline

ABSTRACT: Mapping translation initiation sites by ribosome profiling in primary mouse cortical neurons treated with either DMSO or bicuculline

PROVIDER: PRJNA1073923 | ENA |

REPOSITORIES: ENA

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Mapping translation initiation sites by ribosome profiling in primary mouse cortical neurons treated with either DMSO or bicuculline

Project description:While previous studies suggest that many mRNAs containing more than one translation initiation site (TIS), the biological significance of most alternative TISs and their protein isoform (proteoform) products remains undetermined. Here we show that alternative translation initiation at a CUG and an AUG TIS in neuronal pentraxin receptor (NPR) mRNA produces two proteoforms, and their relative abundance is regulated by both neuronal activity as well as an adjacent RNA secondary structure. Downstream AUG initiation transformed the N-terminal transmembrane domain into a signal peptide, thereby converting NPR to a secreted factor sufficient to promote synaptic clustering of AMPA-type glutamate receptors. Changing the relative proteoform ratio, but not the overall NPR abundance reduces AMPA receptor in parvalbumin (PV)-positive interneurons and induces changes in learning behaviors in mice. In addition to NPR, N-terminal extensions of C1q-like synaptic organizers, mediated by upstream AUU start codons, anchor these otherwise secreted factors to the membrane. Thus, our results uncovered the plasticity of N-terminal signal sequences regulated by alternative TIS usage as a widespread mechanism to diversify protein localization and functions.

2024-09-23 | GSE255191 | GEO

Ribosome profiling reveals sequence-independent post-initiation pausing as a signature of translation

Project description:The journey of a newly synthesized polypeptide starts in the peptidyltransferase center of the ribosome, from where it traverses the exit tunnel. The interior of the ribosome exit tunnel is neither straight nor smooth. How the ribosome dynamics in vivo is influenced by the exit tunnel is poorly understood. Genome-wide ribosome profiling in mammalian cells reveals elevated ribosome density at the start codon and surprisingly the downstream 5th codon position as well. We found that the highly focused ribosomal pausing shortly after initiation is attributed to the geometry of the exit tunnel, as deletion of the loop region from ribosome protein L4 diminishes translational pausing at the 5th codon position. Unexpectedly, the ribosome variant undergoes translational abandonment shortly after initiation, suggesting that there exists an obligatory step between initiation and elongation commitment. We propose that the post-initiation pausing of ribosomes represents an inherent signature of the translation machinery to ensure productive translation.

2021-02-17 | GSE166874 | GEO

Ribosome profiling in archaea reveals leaderless translation, novel translational initiation sites, and ribosome pausing at single codon resolution

Project description:Ribosome profiling in archaea reveals leaderless translation, novel translational initiation sites, and ribosome pausing at single codon resolution

| PRJNA577942 | ENA

Activation of GCN2 by Ribosome Stalling Links Translation Elongation with Translation Initiation

Project description:Activation of GCN2 by Ribosome Stalling Links Translation Elongation with Translation Initiation

| PRJNA317428 | ENA

Ribosome profiling in archaea reveals leaderless translation, novel translational initiation sites, and ribosome pausing at single codon resolution

Project description:Members of the third domain of life, the Archaea, are ubiquitous in all environments on Earth but remain understudied in many aspects including regulatory processes of the central dogma. Archaea present unique biology because they utilize a mosaic of molecular features from both Bacteria and Eukarya, along with unique features. The advent of a high-throughput view of the translation landscape via ribosome profiling in the Bacteria and the Eukarya has illuminated the complexity and previously underappreciated regulation of translation (i.e. translation efficiency, ribosome surveillance, etc.) that potentially has large scale effects on cellular functionality. Here, we developed ribosome profiling in a model archaeon, Haloferax volcanii and elucidated the translational landscape for the first time in the third domain of life. We coupled ribosome profiling with translation inhibitors to: (a) determine the size of the archaeal ribosome footprint, (b) systematically assign translation states of the ribosome to footprint lengths in a mostly leaderless transcriptome, (c) experimentally induce ribosome pauses and clarify the pausing landscape comprehensively, (d) identify putative novel proteins, including small open reading frames (smORFs), and (e) provide evidence that many genes initiate on putative alternative translation start sites (paTSS) around and within open reading frames (ORFs), demonstrating how a microorganism with a gene dense genome can produce proteins with distinct functions using the same gene.

2020-04-27 | GSE138990 | GEO

Ribosome collisions trigger cis-acting feedback inhibition of translation initiation

Project description:Translation of aberrant mRNAs can cause ribosomes to stall, leading to collisions with trailing ribosomes. Collided ribosomes are specifically recognized by ZNF598 to initiate protein and mRNA quality control pathways. Here we found using quantitative proteomics of collided ribosomes that EDF1 is a ZNF598-independent sensor of ribosome collisions. EDF1 recruits and stabilizes GIGYF2 at collisions to inhibit translation initiation in cis via 4EHP. The GIGYF2 axis acts independently of the ZNF598 axis, but each pathway’s output is more pronounced without the other. We propose that the widely conserved and highly abundant EDF1 monitors the transcriptome for excessive ribosome density, then triggers a GIGYF2-mediated response to locally and temporarily reduce ribosome loading. Only when collisions persist is translation abandoned to initiate ZNF598-dependent quality control. This tiered response to ribosome collisions would allow cells to dynamically tune translation rates while ensuring fidelity of the resulting protein products.

2020-07-14 | PXD020239 | Pride

Discovery of non-canonical translation initiation sites through mass spectrometric analysis of protein N-termini

Project description:Translation initiation generally occurs at AUG codons in eukaryotes although it has been shown that non-AUG or non-canonical translation initiation can also occur. However, the evidence for non-canonical translation initiation sites (TISs) is largely indirect and based on ribosome profiling studies. Here, using a strategy specifically designed to enrich N-termini of proteins, we demonstrate that many human proteins are translated at non-canonical TISs. The large majority of TISs that mapped to 5’ untranslated regions were non-canonical and led to N-terminal extension of annotated proteins or translation of upstream small open reading frames (uORF). There has been little controversy on whether the corresponding amino acid to the start codon is incorporated at TIS or methionine is still incorporated. Notably, methionine was incorporated at almost all non-canonical TISs identified in this study. Comparison of the TISs determined through mass spectrometry with ribosome profiling data revealed that about two-thirds of the novel annotations were indeed supported by ribosome profiling data. The sequence orthology analysis and relative translation frequency analysis of non-canonical TISs over canonical ones suggests that those non-canonical TISs are not leaky but they can have certain biological functions. Overall, this study provides evidence of protein translation initiation at non-canonical TISs and indicates that further studies are required for elucidation of functional implications of such non-canonical translation initiation.

2017-11-23 | PXD006633 | Pride

Synonymous codon usage regulates translation initiation

Project description:Ribo-seq with firefly luciferase optimality reporters to determine whether incomplete translation and/or inhibited translation initiation is responsible for the reduced ribosome occupancy on nonoptimal transcripts.

2022-05-16 | GSE202900 | GEO

Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation

Project description:Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation

| PRJNA755697 | ENA

Translation initiation landscape of tomato-infecting virus

Project description:We report the global profile of ribosome profilig to reveal the in vivo translation initiation sites of tomato-infecting virus.

2022-05-04 | GSE160907 | GEO

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