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Small and large ribosomal subunit deficiencies lead to distinct gene expression signatures that reflect cellular growth rate

ABSTRACT: Small and large ribosomal subunit deficiencies lead to distinct gene expression signatures that reflect cellular growth rate

PROVIDER: PRJNA496043 | ENA |

REPOSITORIES: ENA

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Small and large ribosomal subunit deficiencies lead to distinct gene expression signatures that reflect cellular growth rate

Project description:Levels of the ribosome, the conserved molecular machine that mediates translation, are tightly linked to cellular growth rate. In humans, ribosomopathies are diseases associated with cell-type-specific pathologies and reduced ribosomal protein (RP) levels. Because gene expression defects resulting from ribosome deficiency have not yet been experimentally defined, we systematically probed mRNA, translation, and protein signatures that were either unlinked or linked to cellular growth rate in RP-deficient yeast cells. Ribosome concentration was seen to be associated with translation of gene sub-classes, and profound general secondary effects of RP loss on the spectrum of cellular mRNAs were seen. Among these effects, growth-defective 60S mutants increased synthesis of proteins involved in proteasome-mediated degradation, whereas 40S mutants accumulated mature 60S subunits and increased translation of ribosome biogenesis genes. These distinct signatures of protein synthesis suggest intriguing and currently mysterious differences in the cellular consequences of deficiency for small and large ribosomal subunits.

2018-11-29 | GSE121189 | GEO

Small and Large Ribosomal Subunit Deficiencies Lead to Distinct Gene Expression Signatures that Reflect Cellular Growth Rate.

Project description:Levels of the ribosome, the conserved molecular machine that mediates translation, are tightly linked to cellular growth rate. In humans, ribosomopathies are diseases associated with cell-type-specific pathologies and reduced ribosomal protein (RP) levels. Because gene expression defects resulting from ribosome deficiency have not yet been experimentally defined, we systematically probed mRNA, translation, and protein signatures that were either unlinked from or linked to cellular growth rate in RP-deficient yeast cells. Ribosome deficiency was associated with altered translation of gene subclasses, and profound general secondary effects of RP loss on the spectrum of cellular mRNAs were seen. Among these effects, growth-defective 60S mutants increased synthesis of proteins involved in proteasome-mediated degradation, whereas 40S mutants accumulated mature 60S subunits and increased translation of ribosome biogenesis genes. These distinct signatures of protein synthesis suggest intriguing and currently mysterious differences in the cellular consequences of deficiency for small and large ribosomal subunits.

| S-EPMC6382079 | biostudies-literature

Small and large ribosomal subunit deficiencies lead to distinct gene expression signatures that reflect cellular growth rate

2018-10-12 | MSV000083033 | MassIVE

Exosomal RNA may reflect placenta deficiencies and provide better biomarker in preterm birth.

Project description:Exosomal RNA may reflect placenta deficiencies and provide better biomarker in preterm birth.

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Proteome of synthetic ribosomal 40S subunit

Project description:In this study, we present the first methodology (to the best of our knowledge) enabling reconstruction of the eukaryotic 40S ribosome subunit with completely customized r-proteins, referred to as “Ribo-swap” (Figure 1). In Ribo-swap, a designer platform yeast was developed through relocating the 56 genes encoding the whole set of 32 40S r-proteins from native genome loci to a synthetic gene cluster, which could be further swapped by another one encoding customer-designed 40S r-proteins to reconstruct customer 40S ribosome subunits in yeast.

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RNA Post-transcriptional Modifications of an Early-Stage Large Subunit Ribosomal Intermediate

Project description:Protein production by the ribosomes is fundamental to life and proper assembly of the ribosome is required for protein production. The RNA, which is post-transcriptionally modified, provides the platform for ribosome assembly. Thus, a complete understanding of ribosome assembly requires the determination of the RNA post-transcriptional modifications in all the ribosome assembly intermediates and on each pathway. There are 26 RNA post-transcriptional modifications in 23S RNA of the mature Escherichia coli (E.coli) large ribosomal subunit. The levels of these modifications have been investigated extensively only for a small number of large subunit intermediates and under a limited number of cellular and environmental conditions. In this study we determine the level of incorporations of 2-methyl adenosine, 3-methyl pseudouridine, 5-hydroxycytosine and eight pseudouridines in an early-stage E.coli large subunit assembly intermediate with a sedimentation coefficient of 27S. The 27S intermediate is one of three large subunit intermediates accumulated in E.coli cells lacking the DEAD-box RNA helicase DbpA and expressing the helicase inactive R331A DbpA construct. The majority of the investigated modifications are incorporated into the 27S large subunit intermediate to similar levels as in the mature 50S large subunit, indicating that these early modifications or the enzymes that incorporate them have important roles in the initial events of large subunit ribosome assembly.

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Project description:These are the ribosomal subunit fractions from the polysome gradients. investigating effect of heat shock on procyclic-form trypanosomes.

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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.

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Project description:Lead-seq: transcriptome-wide in vivo structure probing with lead

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High-resolution array comparative genomic hybridization of genetic deficiencies on chromosome V in C. elegans

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