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Ribosome profiling study of dom34 and hbs1 knockout strains using short (16-nt) and long (28-nt) monosome-protected footprints and disome-protected footprints

ABSTRACT: Ribosomes that stall before completing peptide synthesis must be recycled and returned to the cytoplasmic pool. The protein Dom34 and cofactors Hbs1 and Rli1 can dissociate stalled ribosomes in vitro, but the identity of targets in the cell is unknown. Here we use ribosome profiling methodology to reveal a high- resolution molecular characterization of Dom34 function in vivo. We show that Dom34 removes stalled ribosomes from mRNAs that are truncated but, in contrast, does not generally dissociate ribosomes on coding sequences known to trigger stalling, such as polyproline. We also show that Dom34 targets arrested ribosomes near the ends of 3 ́ UTRs. These ribosomes appear to gain access to the 3 ́ UTR via a mechanism that does not require decoding of the mRNA. These results suggest that Dom34 carries out the important task of rescuing ribosomes found in noncoding regions.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE52968 | GEO | 2013/12/19

SECONDARY ACCESSION(S): PRJNA230577

REPOSITORIES: GEO

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Ribosome profiling study of dom34 and hbs1 knockout strains using short (16-nt) and long (28-nt) monosome-protected footprints and disome-protected footprints

Project description:Ribosomes that stall before completing peptide synthesis must be recycled and returned to the cytoplasmic pool. The protein Dom34 and cofactors Hbs1 and Rli1 can dissociate stalled ribosomes in vitro, but the identity of targets in the cell is unknown. Here we use ribosome profiling methodology to reveal a high- resolution molecular characterization of Dom34 function in vivo. We show that Dom34 removes stalled ribosomes from mRNAs that are truncated but, in contrast, does not generally dissociate ribosomes on coding sequences known to trigger stalling, such as polyproline. We also show that Dom34 targets arrested ribosomes near the ends of 3 ? UTRs. These ribosomes appear to gain access to the 3 ? UTR via a mechanism that does not require decoding of the mRNA. These results suggest that Dom34 carries out the important task of rescuing ribosomes found in noncoding regions. 25 samples are included in the study (2 mRNA-Seq samples and 23 ribosome footprint profiling samples). These include wild-type and dom34 or hbs1 knockout strains that were created in a variety of genetic backgrounds, treated with various agents in cell culture (e.g. diamide, 3-AT, or glucose starvation), treated differently during cell lysis (use of cycloheximide vs. other ribosome-stabilizing agents), or prepared in different ways after cell lysis (e.g. retention of short vs. long monosome-protected footprints or disome footprints).

2013-12-19 | E-GEOD-52968 | biostudies-arrayexpress

Ribosome profiling study of rli1 depeletion strain

Project description:ABCE1/Rli1 functions as a ribosome recycling factor in vitro, but has not been shown to be crucial for recycling in vivo. We use ribosome profiling and biochemistry to define the role of Rli1 in living yeast. When Rli1 levels were diminished, 80S ribosomes accumulated at stop codons and, surprisingly, in the adjoining 3'UTRs of most genes. While ribosomes did not show preference for any reading frame in the 3'UTR, their enrichment at stop codons and His codons after histidine starvation is consistent with aberrant 3'UTR translation. Predicted 3'UTR translation products were detected by Western analysis and mass spectrometry, and their small sizes indicate a reinitiation mechanism. Eliminating ribosome-rescue factor Dom34 dramatically increases 3'UTR ribosome occupancy in Rli1 depleted cells, indicating that Dom34 clears the bulk of unrecycled ribosomes. Thus, Rli1 is crucial for ribosome recycling in vivo and for overall gene expression as it controls ribosome homeostasis and 3'UTR translation.

2015-06-02 | GSE69414 | GEO

Ribosome profiling study of Dhh1p overexpression and the dhh1 knockout strain using monosome-protected footprints

Project description:A major determinant of mRNA half-life is the codon-dependent rate of translational elongation. How the processes of translational elongation and mRNA decay communicate is unclear. In this study we establish that the DEAD-box helicase Dhh1p is the sensor of codon optimality (i.e. translational elongation rate) that targets an mRNA for decay. First, we find that mRNAs whose translation elongation rate is slowed by inclusion of non-optimal codons are specifically degraded in a DHH1-dependent manner. Biochemical experiments show that Dhh1p is preferentially associated with mRNAs with suboptimal codon choice. We find that these effects on mRNA decay are sensitive to the number of slow moving ribosomes on an mRNA. Using a tethering system, we establish that non-optimal mRNAs become preferentially saturated with ribosomes when Dhh1p is bound. Moreover, over-expression of Dhh1p leads to the accumulation of ribosomes specifically on mRNAs with low codon optimality in ribosome profiling experiments. Lastly, Dhh1p physically interacts with ribosomes in vivo. Together, these data argue that Dhh1p is a sensor for ribosome speed, targeting an mRNA for repression and subsequent decay.

2016-05-11 | GSE81269 | GEO

Genome-wide survey of ribosome collision [monosome/disome]

Project description:In protein synthesis, ribosome movement is not always smooth, rather often impeded by numerous reasons. Although the deceleration of ribosome defines the fates of the mRNAs and the synthesizing proteins, fundamental questions remain to be addressed including where ribosomes pause in mRNAs, what kind of RNA/amino acid context causes the pausing, and how physiologically significant the slowdown of protein synthesis is. Here we surveyed the position of ribosome collisions, caused by ribosome pausing, at a genome-wide level using the modified ribosome profiling in human and zebrafish. The collided ribosomes, i.e. disome, emerge at various sites; the proline-proline-lysine motif, stop codons, and 3′ UTR. The number of ribosomes in a collision is not limited to two, rather four to five, forming a queue of ribosomes. Especially, XBP1, a key modulator of unfolded protein response, shows striking queues of collided ribosomes thus acts as a substrate for ribosome-associated quality control (RQC) to avoid the accumulation of undesired proteins in the absence of stress. Our results provide an insight into the causes and the consequences of ribosome slowdowns by dissecting the specific architecture of ribosomes.

2020-05-05 | GSE133393 | GEO

Analysis of conditions leading to 3'UTR ribosome protected footprints

Project description:Ribosome profiling data from U2OS, HeLa and Kc167 cells under various lysis conditions and using immunoprecipitation to purifiy ribosome associated footprints. Two human cell lines (U2OS and HeLa cells) and a Drosophila melanogaster cell line (Kc167) are used to see if the 3'UTR reads are identified in each cell type. Immunoprecipitation of ribosomes is used to analyse if 3'UTR reads derive from ribosomes (are found with ribosome immunoprecipitates) and to which extent the lysis conditions contribute to the identification of the 3'UTR reads.

2015-01-08 | E-MTAB-3135 | biostudies-arrayexpress

An evolutionarily conserved ribosome-rescue pathway maintains epidermal homeostasis

Project description:mRNA quality control mechanisms ensure fidelity of protein translation. An evolutionarily conserved component of the quality control machinery, Dom34/Pelota (Pelo), rescues stalled ribosomes. Here we show that Pelo is required for mammalian epidermal homeostasis. Our study reveals a novel role for the ribosome-rescue machinery in mammalian tissue homeostasis and an unanticipated specificity in its impact on different stem cell populations.

2018-03-01 | GSE106246 | GEO

Cue2 and Slh1 define parallel pathways to rescue stalled ribosomes

Project description:Ribosome stalling at problematic sequences in mRNAs leads to collisions that trigger a collection of quality control events including ribosome rescue, targeting the nascent polypeptide for decay (Ribosome-mediated Quality Control or RQC), and targeting of the mRNA for decay (No Go Decay or NGD). Using a reverse genetic screen in yeast, we identify Cue2 as the endonuclease that is recruited to stalled ribosomes to promote NGD. Following Cue2-mediated cleavage, ribosomes upstream of the cleavage site translate to the end of the truncated mRNA and are rescued by the Dom34:Hbs1 complex. We also show that the putative helicase Slh1 (part of the RQC Trigger or RQT complex) removes collided ribosomes behind the lead stalled ribosome and thereby reduces endonucleolytic cleavage by Cue2. The synergistic activities of Cue2 and Slh1 define two parallel pathways that allow cells to recognize and respond to ribosomes trapped on problematic mRNAs.

2019-06-25 | GSE129128 | GEO

The landscape of translational stall sites in bacteria revealed by monosome and disome profiling.

Project description:Ribosome pauses are associated with various cotranslational events and determine the fate of mRNAs and proteins. Thus, the identification of precise pause sites across the transcriptome is desirable; however, the landscape of ribosome pauses in bacteria remains ambiguous. Here, we harness monosome and disome (or collided ribosome) profiling strategies to survey ribosome pause sites in Escherichia coli Compared to eukaryotes, ribosome collisions in bacteria showed remarkable differences: a low frequency of disomes at stop codons, collisions occurring immediately after 70S assembly on start codons, and shorter queues of ribosomes trailing upstream. The pause sites corresponded with the biochemical validation by integrated nascent chain profiling (iNP) to detect polypeptidyl-tRNA, an elongation intermediate. Moreover, the subset of those sites showed puromycin resistance, presenting slow peptidyl transfer. Among the identified sites, the ribosome pause at Asn586 of ycbZ was validated by biochemical reporter assay, tRNA sequencing (tRNA-seq), and cryo-electron microscopy (cryo-EM) experiments. Our results provide a useful resource for ribosome stalling sites in bacteria.

| S-EPMC8848927 | biostudies-literature

Translation of poly(A) tails leads to precise mRNA cleavage and widespread ribosome rescue

Project description:Translation of poly(A) tails leads to mRNA cleavage but the mechanism and global pervasiveness of this “nonstop/no-go” decay process is not understood. Here we performed ribosome profiling of short 15-18 nt mRNA footprints to identify ribosomes stalled at 3’ ends of mRNA decay intermediates. We found mRNA cleavage extending hundreds of nucleotides upstream of ribosome stalling in poly(A) and predominantly in one reading frame. These observations suggest that cleavage is closely associated with the ribosome. Surprisingly, ribosomes appeared to stall when as few as 3 consecutive ORF-internal lysine codons were positioned in the A, P, and E sites though significant mRNA degradation was not observed. Endonucleolytic cleavage was widespread, however, at sites of premature polyadenylation and rescue of the ribosomes stalled at these sites was dependent on Dom34. These results suggest this process may be critical when changes in polyadenylation occur during development, tumorigenesis, or when translation termination/recycling is impaired.

2017-01-22 | GSE85944 | GEO

Hcr1/eIF3j is a 60S ribosomal subunit recycling accessory factor in vivo

Project description:Hcr1/eIF3j is a sub-stoichiometric subunit of eukaryotic initiation factor 3 (eIF3) that can dissociate the post-termination 40S ribosomal subunit from mRNA in vitro. We examined this ribosome recycling role in vivo by ribosome profiling and reporter assays and found that loss of Hcr1 led to reinitiation of translation in 3’UTRs, consistent with a defect in recycling. However, the defect appeared to be in recycling of the 60S subunit, rather than the 40S subunit, because reinitiation did not require an AUG codon and was suppressed by overexpression of the 60S dissociation factor Rli1/ABCE1. Consistent with a 60S recycling role, overexpression of Hcr1 could not compensate for loss of 40S recycling factors Tma64/eIF2D and Tma20/MCT-1. Intriguingly, loss of Hcr1 triggered higher expression of RLI1 via an apparent feedback loop. These findings suggest Hcr1/eIF3j is recruited to ribosomes at stop codons and may coordinate the transition to a new round of translation.

2019-05-23 | GSE124204 | GEO

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