ArticleBMC genomics2015
A comparative genomics study on the effect of individual amino acids on ribosome stalling.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed, 80 citations in OpenAlex.
- Structure determination and dual targeting of a plant TACO1 identifies its ancient role as an organelle translation regulator.bioRxiv : the preprint server for biology · 2026Article
- Conserved GTPase OLA1 promotes efficient translation on D/E-rich mRNA.Nature communications · 2025Article
- Reversing the relative time courses of the peptide bond reaction with oligopeptides of different lengths and charged amino acid distributions in the ribosome exit tunnel.Computational and structural biotechnology journal · 2024Article
- A machine learning approach uncovers principles and determinants of eukaryotic ribosome pausing.Science advances · 2024Article
- Synonymous and non-synonymous codon substitutions can alleviate dependence on GroEL for folding.Protein science : a publication of the Protein Society · 2024Article
- Massively parallel identification of sequence motifs triggering ribosome-associated mRNA quality control.Nucleic acids research · 2024Article
- RNA-seq reveals multifaceted gene expression response to Fab production in Escherichia coli fed-batch processes with particular focus on ribosome stalling.Microbial cell factories · 2024Article
- Comprehensive quantitative modeling of translation efficiency in a genome-reduced bacterium.Molecular systems biology · 2023Article
- A strategy to enhance and modify fatty acid synthesis in Corynebacterium glutamicum and Escherichia coli: overexpression of acyl-CoA thioesterases.Microbial cell factories · 2023Article
- The identification of conserved sequence features of co-translationally decayed mRNAs and upstream open reading frames in angiosperm transcriptomes.Plant direct · 2023Article
- Large-scale mRNA translation and the intricate effects of competition for the finite pool of ribosomes.Journal of the Royal Society, Interface · 2022Article
- Innate, translation-dependent silencing of an invasive transposon in Arabidopsis.EMBO reports · 2022Article
- Identification of conserved slow codons that are important for protein expression and function.RNA biology · 2021Article
- Nascent polypeptide within the exit tunnel stabilizes the ribosome to counteract risky translation.The EMBO journal · 2021Article
- Selection for Cheaper Amino Acids Drives Nucleotide Usage at the Start of Translation in Eukaryotic Genes.Genomics, proteomics & bioinformatics · 2021Article
- Deep conservation of ribosome stall sites across RNA processing genes.NAR genomics and bioinformatics · 2021Article
- Full-length ribosome density prediction by a multi-input and multi-output model.PLoS computational biology · 2021Article
- The Multifaceted Roles of Proline in Cell Behavior.Frontiers in cell and developmental biology · 2021Review
- Exploring Potential Signals of Selection for Disordered Residues in Prokaryotic and Eukaryotic Proteins.Genomics, proteomics & bioinformatics · 2020Article
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Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDuring protein synthesis, the nascent peptide chain emerges from the ribosome through the ribosomal exit tunnel. Biochemical interactions between the nascent peptide and the tunnel may stall the ribosome movement and thus affect the expression level of the protein being synthesized. Earlier studies focused on one model organism (S. cerevisiae), have suggested that certain amino acid sequences may be responsible for ribosome stalling; however, the stalling effect at the individual amino acid level across many organisms has not yet been quantified.
resultsBy analyzing multiple ribosome profiling datasets from different organisms (including prokaryotes and eukaryotes), we report for the first time the organism-specific amino acids that significantly lead to ribosome stalling. We show that the identity of the stalling amino acids vary across the tree of life. In agreement with previous studies, we observed a remarkable stalling signal of proline and arginine in S. cerevisiae. In addition, our analysis supports the conjecture that the stalling effect of positively charged amino acids is not universal and that in certain conditions, negative charge may also induce ribosome stalling. Finally, we show that the beginning part of the tunnel tends to undergo more interactions with the translated amino acids than other positions along the tunnel.
conclusionsThe reported results support the conjecture that the ribosomal exit tunnel interacts with various amino acids and that the nature of these interactions varies among different organisms. Our findings should contribute towards better understanding of transcript and proteomic evolution and translation elongation regulation.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.