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TranscriptomicsThe anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria
Protein synthesis by ribosomes takes place on a linear substrate but at variable speeds. Transient pausing of ribosomes can impact a variety of co-translational processes, including protein targeting and folding. These pauses are influenced by the sequence of the mRNA. Thus redundancy in the genetic...
ORGANISM(S): Escherichia coli 
2012-04-01 | E-GEOD-35641 | biostudies-arrayexpress
ProteomicsSuboptimal codon pairs trigger ribosome collisions and cellular quality control responses in tRNA modification mutants
Validation of activation of RQC in U34 tRNA modification mutants by identification of ubiquitination of ribosomal proteins uS3 and uS10.
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2025-12-29 | PXD066757 | Pride
Trna modification  ribosome profiling  protein aggregates  protein homeostasis  ribosome-associated quality control  chaperones  integrated stress response  mrna translation  codon pairs  codon optimality 
UnknownPreferred and avoided codon pairs in three domains of life.
Not available
S-EPMC2585594 | biostudies-literature
ProteomicsChimeric design of Pyrrolysyl-tRNA synthetase/tRNA pairs and canonical synthetase/tRNA pairs for genetic code expansion
An orthogonal aminoacyl-tRNA synthetase/tRNA pair is a key prerequisite for site-specific incorporation of unnatural amino acids. Due to its high codon suppression efficiency and full orthogonality, the pyrrolysyl-tRNA synthetase/pyrrolysyl-tRNA pair is currently the ideal system for genetic code ex...
ORGANISM(S): Escherichia coli 
2020-05-25 | PXD018660 | Pride
Chimeric design Genetic code expansion 
UnknownCodon Pairs are Phylogenetically Conserved: A comprehensive analysis of codon pairing conservation across the Tree of Life.
Not available
S-EPMC7219770 | biostudies-literature
UnknownSuboptimal codon pairs trigger ribosome collisions and cellular quality control responses in tRNA modification mutants.
Not available
S-EPMC12721868 | biostudies-literature
UnknownBias at the third nucleotide of codon pairs in virus and host genomes.
Not available
S-EPMC8927144 | biostudies-literature
TranscriptomicsIdentification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation
Identification of the coding elements in the genome is a fundamental step to understanding the building blocks of living systems. Short peptides (< 100 aa) have emerged as important regulators of development and physiology, but their identification has been limited by their size. We have leveraged t...
ORGANISM(S): Danio rerio 
2014-04-04 | E-GEOD-53693 | biostudies-arrayexpress
OtherCodon Pair-Specific Translation Defects Induce Ribosome-Associated Quality Control to Avoid Proteotoxic Stress [mono_di_profiling]
tRNA modifications tune translation rates and codon optimality, thereby optimizing co-translational protein folding, but how codon optimality defects trigger cellular phenotypes remains unclear. Here, we show that ribosomes stall at specific modification-dependent codon pairs, triggering ribosome co...
ORGANISM(S): Saccharomyces cerevisiae 
2025-12-31 | GSE245671 | GEO
OtherCodon Pair-Specific Translation Defects Induce Ribosome-Associated Quality Control to Avoid Proteotoxic Stress [5P-seq]
tRNA modifications tune translation rates and codon optimality, thereby optimizing co-translational protein folding, but how codon optimality defects trigger cellular phenotypes remains unclear. Here, we show that ribosomes stall at specific modification-dependent codon pairs, triggering ribosome co...
ORGANISM(S): Saccharomyces cerevisiae 
2025-12-31 | GSE245670 | GEO
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