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Translation switch from initiation to elongation needs Not4 and Not5 collaboration

ABSTRACT: Translation switch from initiation to elongation needs Not4 and Not5 collaboration

PROVIDER: PRJNA566006 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10134461.fastq.gz	Fastqsanger.gz
	SRR10134462.fastq.gz	Fastqsanger.gz
	SRR10134463.fastq.gz	Fastqsanger.gz
	SRR10134464.fastq.gz	Fastqsanger.gz
	SRR10134465.fastq.gz	Fastqsanger.gz

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Similar Datasets

Translation switch from initiation to elongation needs Not4 and Not5 collaboration

Project description:Not4 and Not5 are crucial components of the Ccr4-Not complex with pivotal functions in mRNA metabolism. Both associate with ribosomes but mechanistic insights on their function remain elusive. Here we determine that Not5 and Not4 synchronously impact translation initiation and Not5 alone alters translation elongation. Deletion of Not5 causes elongation defects in a codon-dependent fashion, increasing and decreasing the ribosome dwelling occupancy at minor and major codons respectively. This enhanced difference in codon translation velocities alters translation globally and enables normally kinetically unfavorable processes such as nascent chain deubiquitination to take place. In turn this leads to abortive translation and favors protein aggregation. These findings highlight the global impact of Not4 and Not5 in controlling the programmed local speed of mRNA translation.

2021-08-18 | GSE137613 | GEO

Puf3 contributes to changes in mRNA solubility, translation elongation dynamics at rare arginine codons and loss of protein homeostasis in cells lacking Not4

Project description:The Not subunits of the Ccr4-Not complex play an important role in regulating translation elongation dynamics, essential for proper folding and assembly of new proteins. Ribosomes bound by Not5, in complex with Not4, are enriched for non-optimal codons in the A-site. Such ribosomes accumulate in cells lacking Not4 or Not5 that show defects in co-translational assembly and aggregation of new proteins. Recently we observed that rapid depletion of Not1 and Not4 inversely regulates changes in mRNA solubility, correlating with codon-specific changes in A-site ribosome dwelling occupancies (RDOs). Here we describe that mRNAs less soluble upon Not4 depletion but more upon Not1 depletion are enriched for targets of the yeast Puf3 RNA binding protein. We determine that Puf3 is responsible for inverse changes of A-site RDOs upon Not1 and Not4 depletion, in particular at rare arginine codons, and it contributes to changes in mRNA solubility in the absence of Not4. Moreover, deletion of Puf3 suppresses temperature sensitivity and protein aggregation in not4D while overexpression of Puf3 is toxic.

2026-08-26 | GSE303644 | GEO

The Not4 ubiquitin ligase utilizes its conserved RNA binding domains to regulate global proteostasis and RNA polymerase II-dependent transcription

Project description:The conserved Ccr4-Not complex regulates all aspects of the RNA polymerase II (Pol II) gene expression pathway, while it also controls proteasome assembly and function. The Not4 RING domain ubiquitin ligase is a core subunit that also contains an RNA recognition motif (RRM) and C3H1 domain (collectively referred to as the RRM-C) whose function is unknown. Herein, we demonstrate that the Not4 RRM-C contributes to both Not4-dependent regulation of the proteasome and Pol II. Disruption of both Not4 ligase activity and the RRM-C domain simultaneously replicates the proteasome-dependent deubiquitylation and catalytic activity misregulation found in Not4-deficient cells. Transcriptome analysis reveals that the Not4 RRM-C affects a subset of Pol II-dependent genes involved in specific biological functions, including transcription elongation, cyclin-dependent kinase regulated nutrient responses, and ribosomal biogenesis. At these genes, the Not4 RRM-C negatively regulates Pol II binding. While Not4 RRM-C disruption modestly increases between Ccr4-Not and Pol II, a Not4 ligase mutant decreases Ccr4-Not association with Pol II, thus implicating Not4-dependent ubiquitylation in mediating Ccr4-Not interaction with Pol II. Collectively, our results suggests the cellular RNA environment may integrate control of global proteostasis and Pol II transcription through the Not4 ubiquitin ligase.

2017-08-03 | GSE102192 | GEO

Puf3 contributes to changes in mRNA solubility, translation elongation dynamics at rare arginine codons and loss of protein homeostasis in cells lacking Not4

Project description:Here, we describe that Not4 and Puf3 interact to regulate protein homeostasis. mRNAs less soluble upon Not4 depletion but more upon Not1 depletion are enriched for targets of the yeast Puf3 RNA binding protein.

2026-08-26 | GSE305765 | GEO

TOR-NOT4 signalling couples translation to co-translational quality control in plants

Project description:Protein homeostasis (proteostasis) is in part maintained by co-translational quality control mechanisms that prevent errors during protein synthesis by targeting aberrant polypeptides for degradation. While such systems are relatively well-characterized in yeast and animals, their identity and regulation in plants remain poorly understood, and broader knowledge of how organisms synchronise protein production with quality control is lacking. In eukaryotes, the Target of Rapamycin (TOR) kinase drives translation, but a direct link to co-translational surveillance has not been established. Here, we identify three NOT4-like E3 ubiquitin ligases (NOT4A-C) as TOR-regulated factors that coordinate co-translational protein quality control to limit proteotoxic stress in Arabidopsis thaliana. Loss of NOT4 function increases TOR activity and global translation rates, and leads to an accumulation of polyubiquitylated proteins, as well as hypersensitivity to proteasome and TOR inhibition and protein misfolding stress. We found that NOT4A co-localizes with TOR in cytoplasmic foci, and not4 mutants phenocopy TOR-inhibited wild-type plants for a subset of transcriptional and growth-related outputs, indicating that NOT4s are downstream of and essential for normal TOR signalling. Furthermore, we found that elevated translation in NOT4-deficient plants provides enhanced resistance to Pseudomonas syringae pv. Tomato, suggesting a functional interplay between translational quality control and defence against pathogens that suppress host translation. Our study uncovers a previously uncharacterised TOR–NOT4 signalling axis that may act to proportionately couple translational throughput with quality control capacity to safeguard the plant proteome under both optimal and challenged conditions. Since TOR and NOT4-like proteins are conserved in plants, animals, and fungi, we suggest this mechanism may operate more broadly across eukaryotic taxa.

2026-08-11 | GSE319908 | GEO

Not4 and Not5 modulate translation elongation by Rps7A ubiquitination, Rli1 moonlighting, and condensates that exclude eIF5A

Project description:Not4 and Not5 modulate translation elongation by Rps7A ubiquitination, Rli1 moonlighting, and condensates that exclude eIF5A

| PRJNA565947 | ENA

NLRC4 activation needs lncRNA LNCGM1082

Project description:NLRC4 activation needs lncRNA LNCGM1082

| PRJNA725427 | ENA

ARRA Autism Sequencing Collaboration

Project description:ARRA Autism Sequencing Collaboration

| PRJNA74861 | ENA

Co-translational regulation of Mmf1 expression depends upon its mitochondrial targeting, ubiquitination of Egd1 by Not4, Caf130 and NGD: MitoENCay

Project description:The Ccr4-Not complex is a conserved multi protein complex with diverse roles in the mRNA life cycle. Recently we determined that the Not1 and Not4 subunits of Ccr4-Not inversely regulate mRNA solubility and thereby impact dynamics of co-translation events. One mRNA whose solubility is most extremely inversely regulated by Not1 and Not4 is MMF1 encoding a mitochondrial protein that is translated with apparent ribosome pausing. In this work we uncover a mechanism that limits MMF1 overexpression in fermenting yeast and does not require MMF1 5’ or 3’ untranslated sequences but is mediated solely by the MMF1 coding sequence. This mechanism depends upon co-translational targeting of the MMF1 mRNA to the mitochondria, promoted by its mitochondrial targeting sequence, the Egd1 subunit of the NAC complex, the Om14 outer membrane protein and components of the mitochondrial import machinery as well as by Not4. Thereby, levels and translation of the MMF1 mRNA are limited by a mechanism that we have named Mito-ENCay involving ubiquitination of Egd1 by Not4, the Caf130 subunit of the Ccr4-Not complex and RQC. Our results indicate that this mechanism is used for highly expressed mRNAs that depend upon co-translational interactions for appropriate folding, such as ribosomal protein mRNAs in fermenting yeast.

2025-02-13 | GSE206973 | GEO

NEI Refractive Error Collaboration (KORA)

Project description:NEI Refractive Error Collaboration (KORA)

| PRJNA75817 | ENA