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A mini-hairpin shaped nascent peptide blocks translation termination by a distinct mechanism

ABSTRACT: The mini-hairpin shaped nascent peptide that blocks translation termination was found by comprehensive proteomics approach for small ORFs overexpression.

ORGANISM(S): Escherichia Coli

SUBMITTER: Yuhei Chadani

PROVIDER: PXD052430 | JPOST Repository | Mon Feb 17 00:00:00 GMT 2025

REPOSITORIES: jPOST

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			Action	DRS
	EC_CY4_S3.wiff	Wiff
	EC_CY5_S3.wiff	Wiff
	EC_CY5_S3.wiff.scan	Wiff
	EC_CY6_S3.wiff	Wiff
	EC_CY6_S3.wiff.scan	Wiff

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A mini-hairpin shaped nascent peptide blocks translation termination by a distinct mechanism.

Ando Yushin Y Kobo Akinao A Niwa Tatsuya T Yamakawa Ayako A Konoma Suzuna S Kobayashi Yuki Y Nureki Osamu O Taguchi Hideki H Itoh Yuzuru Y Chadani Yuhei Y

Nature communications 20250308 1

Protein synthesis by ribosomes produces functional proteins but also serves diverse regulatory functions, which depend on the coding amino acid sequences. Certain nascent peptides interact with the ribosome exit tunnel to arrest translation and modulate themselves or the expression of downstream genes. However, a comprehensive understanding of the mechanisms of such ribosome stalling and its regulation remains elusive. In this study, we systematically screen for unidentified ribosome arrest pept ...[more]

PMID: 40057501

Similar Datasets

A mini-hairpin shaped nascent peptide blocks translation termination by a distinct mechanism.

Project description:Protein synthesis by ribosomes produces functional proteins but also serves diverse regulatory functions, which depend on the coding amino acid sequences. Certain nascent peptides interact with the ribosome exit tunnel to arrest translation and modulate themselves or the expression of downstream genes. However, a comprehensive understanding of the mechanisms of such ribosome stalling and its regulation remains elusive. In this study, we systematically screen for unidentified ribosome arrest peptides through phenotypic evaluation, proteomics, and mass spectrometry analyses, leading to the discovery of the arrest peptides PepNL and NanCL in E. coli. Our cryo-EM study on PepNL reveals a distinct arrest mechanism, in which the N-terminus of PepNL folds back towards the tunnel entrance to prevent the catalytic GGQ motif of the release factor from accessing the peptidyl transferase center, causing translation arrest at the UGA stop codon. Furthermore, unlike sensory arrest peptides that require an arrest inducer, PepNL uses tryptophan as an arrest inhibitor, where Trp-tRNATrp reads through the stop codon. Our findings illuminate the mechanism and regulatory framework of nascent peptide-induced translation arrest, paving the way for exploring regulatory nascent peptides.

| S-EPMC11890864 | biostudies-literature

Selective stalling of human translation through small molecule engagement of the ribosome nascent chain

Project description:We use ribosome profiling to demonstrate the selectivity of a small molecule, PF-06446846 that inhibits translation of its target by selectively inducing ribosome-stalling in a nascent chain sequence dependent manner.

2017-06-05 | GSE94454 | GEO

Nascent polypeptide within the exit tunnel stabilizes the ribosome to counteract risky translation

Project description:Continuous translation elongation, irrespective of amino acid sequences, is a prerequisite for living organisms to produce their proteomes. However, the risk of elongation abortion is concealed within nascent polypeptide products. For example, negatively charged sequences with occasional intermittent prolines, termed intrinsic ribosome destabilization (IRD) sequences, destabilizes the translating ribosomal complex. Thus, some nascent chain sequences lead to premature translation cessation. Here, we show that most potential IRD sequences in the middle of open reading frames remain cryptic by two mechanisms: the nascent polypeptide itself that spans the exit tunnel and its bulky amino acid residues that occupy the tunnel entrance region. Thus, nascent polypeptide products have a built-in ability to ensure elongation continuity by serving as a bridge and thus by protecting the large and small ribosomal subunits from dissociation.

2021-12-08 | GSE184331 | GEO

RNA-seq of total and nascent RNA after depletion of Mpe1

Project description:To test the role of Mpe1 in transcription termination we inserted a mini-auxin induced degron (mAID) at the C-terminal end of the endogenous MPE1 locus in the yeast Saccharomyces cerevisiae. We treated Mpe1-mAID cells (JRY101) or wild type cells (WT, YMK728) with 1 mM auxin for 30 minutes and labeled the nascent RNA with 4-thiouracil (4tU) for 6 minutes. The nascent RNA fraction was prepared by biotinylating the 4tU-labeled RNA followed purification with streptavidin beads. Nascent and total RNA fractions were depleted of ribosomal RNA and strand-specific libraries prepared. Libraries were single-end sequenced using an Ilummina HiSeq 4000 instrument.

2021-12-31 | E-MTAB-10820 | biostudies-arrayexpress

Nascent peptide assists the ribosome in recognizing chemically distinct small molecules.

Project description:Regulation of gene expression in response to the changing environment is critical for cell survival. For instance, binding of macrolide antibiotics to the ribosome promotes translation arrest at the leader open reading frames ermCL and ermBL, which is necessary for inducing the antibiotic resistance genes ermC and ermB. Cladinose-containing macrolides such as erythromycin (ERY), but not ketolides such as telithromycin (TEL), arrest translation of ermCL, whereas either ERY or TEL stall ermBL translation. How the ribosome distinguishes between chemically similar small molecules is unknown. We show that single amino acid changes in the leader peptide switch the specificity of recognition of distinct molecules, triggering gene activation in response to ERY alone, to TEL alone or to both antibiotics or preventing stalling altogether. Thus, the ribosomal response to chemical signals can be modulated by minute changes in the nascent peptide, suggesting that protein sequences could have been optimized for rendering translation sensitive to environmental cues.

| S-EPMC5726394 | biostudies-literature

Nascent peptide side chains induce rearrangements in distinct locations of the ribosomal tunnel.

Project description:Although we have numerous structures of ribosomes, none disclose side-chain rearrangements of the nascent peptide during chain elongation. This study reports for the first time that rearrangement of the peptide and/or tunnel occurs in distinct regions of the tunnel and is directed by the unique primary sequence of each nascent peptide. In the tunnel mid-region, the accessibility of an introduced cysteine to a series of novel hydrophilic maleimide reagents increases with increasing volume of the adjacent chain residue, a sensitivity not manifest at the constriction and exit port. This surprising result reveals molecular movements not yet resolvable from structural studies. These findings map solvent-accessible volumes along the tunnel and provide novel insights critical to our understanding of allosteric communication within the ribosomal tunnel, translational arrest, chaperone interaction, folding, and rates of elongation.

| S-EPMC3143575 | biostudies-literature

Role of the Visual Conditioning-Dependent Nascent Proteome in Neuronal Plasticity

Project description:Experience-dependent synaptic plasticity refines brain circuits during development. To uncover protein synthesis-dependent mechanisms contributing to experience-dependent plasticity, we performed quantitative proteomic analysis of the nascent proteome using improved bio-orthogonal metabolic labeling (BONCAT) to identify candidate plasticity proteins (CPPs) that undergo differential protein synthesis in response to visual conditioning (VC) in Xenopus optic tectum. We identified 83 CPPs that formed strongly connected networks and were annotated to a variety of biological functions, including RNA splicing, protein translation, and chromatin remodeling. Functional analysis of select CPPs using translation blocking morpholinos revealed the requirement of eukaryotic initiation factor 3 subunit A (eIF3A), fused in sarcoma (FUS), and ribosomal protein s17 (RPS17) in experience-dependent structural plasticity of tectal neurons. These results demonstrate that the nascent proteome is dynamic in response to VC and that de novo synthesis of the machinery that regulates gene expression and protein translation is required for experience-dependent structural plasticity.

2017-11-21 | MSV000081728 | MassIVE

Proteome-wide analysis of elongating nascent polypeptide chains – peptide pulldown

Project description:Cellular global translation is often measured using ribosome profiling or quantitative mass spectrometry, but these methods do not provide direct information at the level of elongating nascent polypeptide chains (NPCs) and associated co-translational events. We combine quantitative proteomics, pulse labeling with puromycin, and stable isotope-labeled amino acids to analyze thousands of NPCs. Our approach enables global analyses of translational responses and co-translational modifications, providing a framework for dissecting co-translational regulations proteome-wide. The inputs (without IP) were analyzed in triplicates.

2022-05-28 | PXD026349 | JPOST Repository

Nascent RNA sequencing reveals distinct features in Plant transcription

Project description:Transcriptional regulation of gene expression is a major mechanism utilized by plants to confer phenotypic plasticity, yet compared to archaebacteria, eubacteria, and other eukaryotes, very little is known about the design principles of plant transcription. We generated an extensive catalog of nascent and steady state transcripts in Arabidopsis thaliana seedlings using global nuclear run-on sequencing (GRO-seq), 5'GRO-seq and RNA-seq and reanalyzed published maize data to capture the general characteristics of plant transcription. De novo annotation of nascent transcripts enabled accurate start site annotations and revealed novel unstable transcripts. Coding and non-coding transcripts exhibit comparable promoter chromatin configurations. Motif analysis revealed new regulatory DNA elements including a conserved 'TGT core promoter motif' and unreported transcription factor (TF) binding sites. Mapping of engaged RNA polymerases revealed a lack of enhancer RNAs, promoter proximal pausing, and divergent transcription in Arabidopsis and maize, which are commonly present in humans and yeast. In contrast, Arabidopsis and maize genes accumulate RNA polymerases adjacent to the polyadenylation site immediately downstream of genes, a trend that correlated with increasing gene length and coincided with hypomethylation of CpG residues. Lack of promoter proximal pausing and a higher correlation of nascent and steady state transcripts indicates Arabidopsis regulates transcription predominantly at the level of initiation. Together, these findings provide insight into plant transcriptional mechanisms, but also eukaryotic transcription in general.

2016-10-06 | GSE83108 | GEO

Post-transcriptional buffering of low nascent RNA transcription by Puf5

Project description:Gene expression is a dynamic process regulated on several layers starting with transcription, mRNA export, translation and finally, mRNA degradation. While subsequent layers heavily influence each other, it is not clear if the most extreme layers, chromatin architecture and mRNA decay are linked. Here, we show that changes in nascent transcription mediated by mutating H3K56 to alanine are buffered at a post-transcriptional level by the Pumilio protein Puf5, which stabilizes transcripts in a context-dependent manner. Depleting Puf5 in an H3K56A background leads to downregulation of its direct targets, largely consisting of ribosomal protein genes. This is followed by a decrease in translation efficiency and finally, cell cycle arrest. Importantly, we show that this phenomenon of post-transcriptional buffering is not only linked to H3K56A, but might be a more widespread phenomenon to ensure physiological mRNA levels and to maintain cellular homeostasis.

2021-07-19 | E-MTAB-10107 | biostudies-arrayexpress

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