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Translation initiation of the MgtL leader peptide is essential for the expression of mgtA in Escherichia coli

ABSTRACT: Translation initiation of the MgtL leader peptide is essential for the expression of mgtA in Escherichia coli

PROVIDER: PRJNA841499 | ENA |

REPOSITORIES: ENA

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Translation initiation of the MgtL leader peptide is essential for the expression of mgtA in Escherichia coli

Project description:Riboswitches are cis-acting regulating RNA elements mostly found in the 5’-UTR of bacterial mRNAs. The Salmonella enterica mgtA riboswitch controls mgtA expression upon the sensing of intracellular Mg2+ ions. A leader peptide (MgtL) is contained within the mgtA riboswitch and its translation has been previously shown to be affected by Mg2+ concentrations. The current regulatory model suggests that the efficiency of MgtL translation is inversely related to mgtA transcription. Herein we show that the orthologue mgtA riboswitch of Escherichia coli also contains a leader peptide but, unlike S. enterica, that its translation is proportionally related to mgtA expression. Our results also suggest that ribosome stalling at mgtL is crucial for mgtA expression. Together, our results indicate that in E. coli, the expression of the MgtL leader peptide and mgtA are positively coordinated according to the intracellular Mg2+ concentration, a unique mechanism among known riboswitches.

2023-05-01 | GSE203590 | GEO

Synonymous codon usage regulates translation initiation

Project description:Synonymous codon usage regulates translation initiation

| PRJNA837608 | ENA

An antibiotic-sensing leader peptide regulates translation and premature Rho-dependent transcription termination of the topAI gene in Escherichia coli

Project description:An antibiotic-sensing leader peptide regulates translation and premature Rho-dependent transcription termination of the topAI gene in Escherichia coli

| PRJEB34533 | ENA

Loss of function cancer associated mutations in the EIF4G2 non canonical translation initiation factor

Project description:Tumor cells often exploit the protein translation machinery, resulting in enhanced protein expression essential for tumor growth. Since canonical translation initiation is often suppressed due to cell stress in the tumor microenvironment, non-canonical translation initiation mechanisms become particularly important for shaping the tumor proteome. EIF4G2 is a non-canonical translation initiation factor that mediates internal ribosome entry site (IRES) and upstream open reading frame (uORF) dependent initiation mechanisms, which can be used to modulate protein expression in cancer. Here we explored the contribution of EIF4G2 to cancer by screening the COSMIC database for EIF4G2 somatic mutations in cancer patients.

2023-08-21 | MSV000092704 | MassIVE

Translation initiation site profiling reveals widespread synthesis of non-AUG-initiated protein isoforms in yeast

Project description:Genomic analyses in budding yeast have helped to define the foundational principles of eukaryotic gene expression, but have systematically excluded specific classes of potential coding regions, including those with non-AUG start codons. Without methods to define coding regions empirically, the prevalence of these non-canonical coding regions has been impossible to assess. Here, we applied an experimental approach to globally annotate translation initiation sites in yeast and identified a class of 149 genes that encode N-terminally extended alternate protein isoforms that result from translation initiation at non-AUG codons upstream of the annotated AUG start codon. These alternate isoforms are produced in concert with canonical isoforms and are translated with a high degree of specificity, resulting from initiation at only a small subset of possible start codons in 5’ leader regions. Their translation is enriched during meiosis, and is induced by low eIF5A levels, which are observed in this context. These findings reveal widespread production of non-canonical protein isoforms and, more generally, show unexpected complexity to the rules by which the budding yeast genome is decoded.

2020-07-24 | GSE150375 | GEO

Deep sequencing reveals mRNA recruitment in translation initiation

Project description:We studied the initiation signals located in the translational initiation region (TIR) and identified the role for recognition of the initiation signals in each individual stage during formation of the initiation complexes. Sequencing the randomized mRNA libraries captured by translation initiation complexes

2016-07-27 | E-GEOD-69782 | biostudies-arrayexpress

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

The RNA helicase Ded1p suppresses translation initiation from near-cognate start codons

Project description:The conserved and essential DEAD-box RNA helicase Ded1p from yeast and its mammalian ortholog DDX3 are critical for translation initiation. Mutations in DDX3 are linked to tumorigenesis and intellectual disability, and the enzyme is targeted by diverse viruses. How Ded1p and its orthologs engage RNAs to impact translation initiation has been a longstanding, unresolved question. Here we show that Ded1p associates with the pre-initiation complex at the mRNA entry channel of the small ribosomal subunit and that the helicase unwinds mRNA structure ahead of the scanning pre-initiation complex. Defective Ded1p causes pervasive translation in 5’UTRs, starting from near-cognate initiation codons located 5' of mRNA structures and concomitant decrease of protein synthesis from of the main ORFs. The data indicate that Ded1p functions to suppress translation initiation on near-cognate codons proximal to mRNA structure and show how the helicase is targeted to specific RNA sites without common sequence signatures. Our results reveal a straightforward mechanism for the activation of upstream open reading frames and suggest that mRNA structure and proximal near-cognate initiation codons encode a widespread regulatory program for translation initiation that is sensitive to RNA helicase function.

2017-01-24 | GSE93959 | GEO

Translation initiation landscape of tomato-infecting virus

Project description:Translation initiation landscape of tomato-infecting virus

| PRJNA674822 | ENA

Synonymous codon usage regulates translation initiation

Project description:Ribo-seq with firefly luciferase optimality reporters to determine whether incomplete translation and/or inhibited translation initiation is responsible for the reduced ribosome occupancy on nonoptimal transcripts.

2022-05-16 | GSE202900 | GEO

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