Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Khan2018 - Origins of robustness in translational control via eukaryotic translation initiation factor (eIF) 2

ABSTRACT: This is a ordinary differential equation-based model of the eukaryotic translation initiation factor (eIF2) phosphorylation pathway, a pathway important for regulating protein synthesis activity in eukaryotic cells. This model is geared towards identification the principal robustness-conferring features of the pathway.

SUBMITTER: Johannes Meyer

PROVIDER: MODEL1911120001 | BioModels | 2019-11-13

REPOSITORIES: BioModels

ACCESS DATA

Json Xml

Publications

Origins of robustness in translational control via eukaryotic translation initiation factor (eIF) 2.

Khan Mohammad Farhan MF Spurgeon Sarah S von der Haar Tobias T

Journal of theoretical biology 20180221

Phosphorylation of eukaryotic translation initiation factor 2 (eIF2) is one of the best studied and most widely used means for regulating protein synthesis activity in eukaryotic cells. This pathway regulates protein synthesis in response to stresses, viral infections, and nutrient depletion, among others. We present analyses of an ordinary differential equation-based model of this pathway, which aim to identify its principal robustness-conferring features. Our analyses indicate that robustness ...[more]

PMID: 29476830

Similar Datasets

Eukaryotic translation initiation factor 5A regulates autophagy via translation of ATG3

Project description:Autophagy is an essential catabolic process responsible for recycling of intracellular material and preserving cellular fidelity. Key to the autophagy pathway is the ubiquitin-like conjugation system mediating lipidation of Atg8 proteins and their anchoring to autophagosomal membranes. While regulation of autophagy has been characterized at the level of transcription, protein interactions and post-translational modifications, its translational regulation remains elusive. Here we describe a novel regulatory axis of autophagy at the translational level, guided by the conserved eukaryotic translation factor eIF5A. Identified from a high-throughput screen, we find that eIF5A is required for lipidation of LC3B and its paralogs and promotes autophagosome formation. This feature is evolutionarily conserved and results from the translation of the E2-like ATG3 protein. Mechanistically, we identify an amino acid motif in ATG3 causing eIF5A-dependency for its efficient translation. Our study identifies a key regulatory mechanism of autophagosome formation and demonstrates the impact of translation in the regulation autophagy.

2018-04-27 | PXD008874 | Pride

Selective translation mechanism through two paralogs of eukaryotic initiation factor 4A

Project description:Eukaryotic initiation factor (eIF) 4A is a DEAD-box RNA-binding protein that plays a pivotal role in translation initiation. Although mammals have two eIF4A paralogs, eIF4A1 and eIF4A2, their redundancy has been long assumed because of high homology and their functional difference has been poorly understood. Here we show that eIF4A paralogs employ differential translation programs. Ribosome profiling of eIF4A1- and eIF4A2-knockout HEK293T cell lines revealed that translation efficiency changes were divergent across transcriptome and distinct group of mRNAs were regulated by each paralog. Our analysis indicates that eIF4A1 and eIF4A2 facilitate translation of specific mRNAs.

2019-10-26 | GSE126298 | GEO

The eukaryotic translation initiation factor eIF4E regulates flowering and circadian rhythm in Arabidopsis

Project description:Translation initiation is a rate-limiting step in protein synthesis. The eukaryotic translation initiation factor 4E (eIF4E) plays an essential role in the translation initiation process. However, how eIF4E-dependent translation initiation regulates plant growth and development remains not fully understood. In this study, we have found that Arabidopsis eIF4E proteins distribute both in the nucleus and cytoplasm, and only cytoplasmic eIF4E is implicated in the control of flowering time. Results of profiling the genome-wide translation by Ribo-tag sequencing further reveal that eIF4E may regulate plant flowering by affecting homeostatic translation of flowering-time genes, including the Central Oscillator Genes (COGs). Consistent with the hypothesis that transcription-translation feedback loop is the core mechanism to drive the oscillation of circadian clock, we show that the eIF4E-dependent translation modulates the rhythmic oscillation of protein abundance of the clock-related genes (CCGs). Together, our study provides mechanistic insights into how the protein translation regulates multiple developmental processed in Arabidopsis including circadian clock and photoperiodic flowering.

2023-10-25 | GSE245858 | GEO

Translational control of depression-like behavior via phosphorylation of eukaryotic translation initiation factor 4E.

Project description: Not available

| S-EPMC6018502 | biostudies-literature

The eukaryotic translation initiation factor eIF4E elevates steady-state m7G capping of coding and noncoding transcripts

Project description:Methyl-7-guanosine (m7G) “capping” of coding and some noncoding RNAs is critical for their maturation and subsequent activity. Here, we discovered that eukaryotic translation initiation factor 4E(eIF4E), itself a cap-binding protein, drives the expression of the capping machinery and the increased capping efficiency of ∼100 coding and noncoding RNAs. This dataset collects transcriptomic data for quantitative cap immunoprecipitation (CapIP) assay in eIF4E-Flag or vector stable U2Os cells.

2020-09-30 | GSE158728 | GEO

USP9X controls translation efficiency via deubiquitination of eukaryotic translation initiation factor 4A1.

Project description: Not available

| S-EPMC5778534 | biostudies-literature

Project description:Eukaryotic translation initiation factor 4E (eIF4E)–binding protein 1 (4E-BP1) inhibits cap-dependent translation in eukaryotes by competing with eIF4G for an interaction with eIF4E. Phos-phorylation at Ser-83 of 4E-BP1 occurs during mitosis through the activity of cyclin-dependent kinase 1 (CDK1)/cyclin B rather than through canonical mTOR kinase activity. Here, we investi-gated the interaction of eIF4E with 4E-BP1 or eIF4G during interphase and mitosis. We observed that 4E-BP1 and eIF4G bind eIF4E at similar levels during interphase and mitosis. The most highly phosphorylated mitotic 4E-BP1 isoform (δ) did not interact with eIF4E, whereas a distinct 4E-BP1 phospho-isoform, EB-γ—phosphorylated at Thr-70, Ser-83, and Ser-101—bound to eIF4E during mitosis. Two-dimensional gel electropho-retic analysis corroborated the identity of the phosphorylation marks on the eIF4E-bound 4E-BP1 isoforms and uncovered a population of phosphorylated 4E-BP1 molecules lacking Thr-37/Thr-46–priming phosphorylation. Moreover, proximity ligation assays for phospho–4E-BP1 and eIF4E revealed different in situ interactions during interphase and mitosis. The eIF4E:eIF4G interaction was not inhibited, but rather increased in mitotic cells, consistent with active translation initiation during mitosis. Phospho-defective substitution of 4E-BP1 at Ser-83 did not change global translation or individual mRNA translation profiles as measured by single-cell nascent protein synthesis and eIF4G RNA-immunoprecipitation sequencing. Mitotic 5’-terminal oligopyrimidine RNA translation was active and, unlike interphase translation, resistant to mTOR inhibition. Our findings reveal the phosphorylation profiles of 4E-BP1 isoforms and their interactions with eIF4E throughout the cell cycle and indicate that 4E-BP1 does not specifically inhibit translation initiation during mitosis.

2019-06-14 | GSE131668 | GEO

Selective translation mechanism through two paralogs of eukaryotic initiation factor 4A

Project description:Selective translation mechanism through two paralogs of eukaryotic initiation factor 4A

| PRJNA521496 | ENA

Cellular translational enhancer elements that recruit eukaryotic initiation factor 3

Project description:Translation initiation is a highly regulated process which broadly affects eukaryotic gene expression. Eukaryotic initiation factor 3 (eIF3) is a central player in canonical and alternative pathways for ribosome recruitment. Here we have investigated how direct binding of eIF3 contributes to the large and regulated differences in protein output conferred by different 5′-untranslated regions (5′-UTRs) of cellular mRNAs. Using an unbiased high-throughput approach to determine the affinity of budding yeast eIF3 for native 5′-UTRs from 4,252 genes, we demonstrate that eIF3 binds specifically to a subset of 5′-UTRs that contain a short unstructured binding motif, AMAYAA. eIF3 binding mRNAs have higher ribosome density in growing cells and are preferentially translated under certain stress conditions, supporting the functional relevance of this interaction. Our results reveal a new class of translational enhancer and suggest a mechanism by which changes in core initiation factor activity enact mRNA-specific translation programs.

2022-07-06 | GSE180046 | GEO

Translation elongation can control translation initiation on eukaryotic mRNAs.

Project description: Not available

| S-EPMC3990680 | biostudies-literature