ArticleThe Journal of biological chemistry2014
Comprehensive analysis of stop codon usage in bacteria and its correlation with release factor abundance.
Article in The Journal of biological chemistry, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed, 88 citations in OpenAlex.
- The mycobacterial selenocysteine machinery: presence and expression.RNA biology · 2026Article
- Stop codon reassignment to tryptophan in members of the bacterial phylumMicrobial genomics · 2026Article
- Reshaping organellar translation and tRNA metabolism: the consequences of photosynthesis loss and massive horizontal gene transfer.Molecular biology and evolution · 2026Article
- Genetic constraints on protein loop evolution: out-of-frame stop codons limitFrontiers in molecular biosciences · 2026Article
- Article
- Suppression of amber stop codons impairs pathogenicity in Salmonella.FEBS letters · 2025Article
- Sequence modeling and design from molecular to genome scale with Evo.Science (New York, N.Y.) · 2024Article
- Fluorescent reporters give new insights into antibiotics-induced nonsense and frameshift mistranslation.Scientific reports · 2024Article
- Transient disome complex formation in native polysomes during ongoing protein synthesis captured by cryo-EM.Nature communications · 2024Article
- Analysis of programmed frameshifting during translation ofRNA (New York, N.Y.) · 2024Article
- Genes for highly abundant proteins in Escherichia coli avoid 5' codons that promote ribosomal initiation.PLoS computational biology · 2023Article
- Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance.Cell reports · 2023Article
- Evolution of termination codons of proteins and the TAG-TGA paradox.Scientific reports · 2023Article
- Epistasis between promoter activity and coding mutations shapes gene evolvability.Science advances · 2023Article
- INRI-seq enables global cell-free analysis of translation initiation and off-target effects of antisense inhibitors.Nucleic acids research · 2022Article
- Complete Mitochondrial Genome Sequences of Korean Phytophthora infestans Isolates and Comparative Analysis of Mitochondrial Haplotypes.The plant pathology journal · 2022Article
- Stop Codon Usage as a Window into Genome Evolution: Mutation, Selection, Biased Gene Conversion and the TAG Paradox.Genome biology and evolution · 2022Article
- Unusual mammalian usage of TGA stop codons reveals that sequence conservation need not imply purifying selection.PLoS biology · 2022Article
- Genetic Determinants of Tigecycline Resistance inAntibiotics (Basel, Switzerland) · 2022Review
- Why Is the UAG (Amber) Stop Codon Almost Absent in Highly Expressed Bacterial Genes?Life (Basel, Switzerland) · 2022Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a comprehensive analysis of stop codon usage in bacteria by analyzing over eight million coding sequences of 4684 bacterial sequences. Using a newly developed program called "stop codon counter," the frequencies of the three classical stop codons TAA, TAG, and TGA were analyzed, and a publicly available stop codon database was built. Our analysis shows that with increasing genomic GC content the frequency of the TAA codon decreases and that of the TGA codon increases in a reciprocal manner. Interestingly, the release factor 1-specific codon TAG maintains a more or less uniform frequency (∼20%) irrespective of the GC content. The low abundance of TAG is also valid with respect to expression level of the genes ending with different stop codons. In contrast, the highly expressed genes predominantly end with TAA, ensuring termination with either of the two release factors. Using three model bacteria with different stop codon usage (Escherichia coli, Mycobacterium smegmatis, and Bacillus subtilis), we show that the frequency of TAG and TGA codons correlates well with the relative steady state amount of mRNA and protein for release factors RF1 and RF2 during exponential growth. Furthermore, using available microarray data for gene expression, we show that in both fast growing and contrasting biofilm formation conditions, the relative level of RF1 is nicely correlated with the expression level of the genes ending with TAG.
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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.