Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RRF plays critical roles in ribosome homeostasis in E. coli but has little effect on translational coupling

ABSTRACT: RRF plays critical roles in ribosome homeostasis in E. coli but has little effect on translational coupling

PROVIDER: PRJNA636967 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

RRF plays critical roles in ribosome homeostasis in E. coli but has little effect on translational coupling

Project description:We used ribosome profiling to characterize the biological role of ribosome recycling factor (RRF) in Escherichia coli. As expected, RRF depletion leads to enrichment of post-termination 70S complexes in 3′-UTRs. We also observe that elongating ribosomes are unable to complete translation because they are blocked by non-recycled ribosomes at stop codons. Previous studies have suggested a role for recycling in translational coupling within operons; if a ribosome remains bound to an mRNA after termination, it may re-initiate downstream. We found, however, that RRF depletion did not significantly affect coupling efficiency in reporter assays or in ribosome density genome-wide. These findings argue that re-initiation is not a major mechanism of translational coupling in E. coli. Finally, RRF depletion has dramatic effects on the activity of ribosome rescue factors tmRNA and ArfA. Our results provide a global view of the effects of the loss of ribosome recycling on protein synthesis in E. coli.

2020-10-06 | GSE151688 | GEO

Ribosome recycling is not critical for translational coupling in Escherichia coli.

Project description: Not available

| S-EPMC7538156 | biostudies-literature

The molecular basis of coupling between poly(A)-tail length and translational efficiency

Project description:In animal oocytes and early embryos, mRNA poly(A)-tail length strongly influences translational efficiency (TE), but later in development this coupling between tail length and TE disappears. Here, we elucidate how this coupling is first established and why it disappears. Overexpressing cytoplasmic poly(A)-binding protein (PABPC) in frog oocytes specifically improved translation of short-tailed mRNAs, thereby diminishing coupling between tail length and TE. Thus, coupling requires limiting PABPC, implying that in coupled systems longer-tail mRNAs better compete for limiting PABPC. In addition to expressing excess PABPC, post-embryonic cells had two other properties that prevented strong coupling: terminal-uridylation-dependent destabilization of mRNAs lacking bound PABPC, and a regulatory regime wherein PABPC contributes minimally to TE. Thus, these results revealed three fundamental mechanistic requirements for coupling and defined the context-dependent functions for PABPC, in which this protein promotes TE but not mRNA stability in coupled systems and mRNA stability but not TE in uncoupled systems.

2021-07-07 | GSE166544 | GEO

Miscanthus sinensis strain:Little Nickey | cultivar:Little Nickey

Project description:Miscanthus sinensis Little Nickey genome sequencing

| PRJNA337042 | ENA

Chaperone-like protein DAY plays critical roles in photomorphogenesis

Project description:Chaperone-like protein DAY plays critical roles in photomorphogenesis

| PRJNA736856 | ENA

Disome-seq reveals sequence-mediated coupling of translational pauses and protein structures

Project description:The regulation of translation elongation plays a vital role in protein folding; an adequate translational pause provides time and cellular environments for the co-translational folding of nascent peptides. However, the genomic landscape, sequence determinants, and molecular consequences of translational pausing remain mostly unknown. In this study, we performed disome-seq that sequenced mRNA fragments protected by two consecutive ribosomes – a product of severe translational pauses during which the upstream ribosome collides into the paused one. We detected severe translational pauses on ~75% of yeast genes. These pauses were often explained by one of the three mechanisms: 1) slow ribosome releasing at stop codons, 2) slow peptide formation from proline, glycine, asparagine, and cysteine, and 3) slow leaving of polylysine from the exit tunnel of ribosomes. Notably, these amino acids also terminate the α-helical conformation. Such dual roles of amino acids establish an inborn coupling between the synthetic completion of a structural motif and a translational pause. Furthermore, paused ribosomes often recruit chaperones to assist protein folding. As a consequence, emergent protein structures during evolution should be ready to be correctly folded. Collectively, our study shows widespread translational pauses and sheds lights on a better understanding of the regulation of co-translational protein folding.

2020-12-10 | PXD015271 | Pride

MEC coupling AD-1

Project description:MEC coupling AD-1 Raw sequence reads

| PRJNA482710 | ENA

Notch Signaling Plays an Instructive Role in Supporting Cell Development and is Critical for Supporting Cell Survival

Project description:The sensory epithelium of the cochlea is a specialized structure responsible for the perception of sound. While much is understood about the development of the mechanosensory hair cells found within this epithelium, little is known about the development of the glial-like supporting cells. Here, we provide evidence that in addition to its well-characterized inhibitory function, canonical Notch signaling plays a positive, instructive role in the differentiation of supporting cells. Using γ-secretase inhibitor DAPT to acutely block canonical Notch signaling, we identified a cohort of Notch-regulated supporting cell-specific genes, with diverse functions in cell signaling, cell differentiation, neuronal innervation and synaptogenesis.

2016-02-01 | GSE67085 | GEO

Glutamine Anabolism Plays a Critical Role in Pancreatic Cancer by Coupling Carbon and Nitrogen Metabolism.

Project description: Not available

| S-EPMC6886125 | biostudies-literature

Janus kinase 1 plays a critical role in mammary cancer progression

Project description:Janus kinase 1 plays a critical role in mammary cancer progression

| PRJNA495488 | ENA