ArticleJournal of molecular evolution1996
The close proximity of Escherichia coli genes: consequences for stop codon and synonymous codon use.
Article in Journal of molecular evolution, 1996. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 44 citations in OpenAlex.
- Lost in translation: conserved amino acid usage despite extreme codon bias in foraminifera.mBio · 2025Article
- Patterns of Change in Nucleotide Diversity Over Gene Length.Genome biology and evolution · 2024Article
- Article
- The role of nucleotide composition in premature termination codon recognition.BMC bioinformatics · 2016Article
- Highly reproductive Escherichia coli cells with no specific assignment to the UAG codon.Scientific reports · 2015Article
- Overlapping genes: a window on gene evolvability.BMC genomics · 2014Article
- Changes in transcriptional orientation are associated with increases in evolutionary rates of enterobacterial genes.BMC bioinformatics · 2011Article
- Stops making sense: translational trade-offs and stop codon reassignment.BMC evolutionary biology · 2011Article
- Classification of bacteria based on the biases of terminal amino acid residues.The protein journal · 2011Article
- Adaptation of the short intergenic spacers between co-directional genes to the Shine-Dalgarno motif among prokaryote genomes.BMC genomics · 2009Article
- Selection for minimization of translational frameshifting errors as a factor in the evolution of codon usage.Nucleic acids research · 2009Article
- PairWise Neighbours database: overlaps and spacers among prokaryote genomes.BMC genomics · 2009Article
- Evolution of gene overlaps: relative reading frame bias in prokaryotic two-component system genes.Journal of molecular evolution · 2007Article
- Intragenic spatial patterns of codon usage bias in prokaryotic and eukaryotic genomes.Genetics · 2004Article
- Hierarchy of sequence-dependent features associated with prokaryotic translation.Genome research · 2003Article
- Correlations between Shine-Dalgarno sequences and gene features such as predicted expression levels and operon structures.Journal of bacteriology · 2002Article
- Stop codons preceded by rare arginine codons are efficient determinants of SsrA tagging in Escherichia coli.Proceedings of the National Academy of Sciences of the United States of America · 2002Article
- Gradients in nucleotide and codon usage along Escherichia coli genes.Nucleic acids research · 2000Article
- Natural selection on synonymous sites is correlated with gene length and recombination in Drosophila.Genetics · 1999Article
- Codon bias in Escherichia coli: the influence of codon context on mutation and selection.Nucleic acids research · 1997Article
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Authors and funding
1 author at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
It is shown that synonymous codon usage is less biased in favor of those codons preferred by highly expressed genes at the end of Escherichia coli genes than in the middle. This appears to be due to the close proximity of many E. coli genes. It is shown that a substantial number of genes overlap either the Shine-Dalgarno sequence or the coding sequence of the next gene on the chromosome and that the codons that overlap have lower synonymous codon bias than those which do not. It is also shown that there is an increase in the frequency of A-ending codons, and a decrease in the frequency of G-ending codons at the end of E. coli genes that lie close to another gene. It is suggested that these trends in composition could be associated with selection against the formation of mRNA secondary structure near the start of the next gene on the chromosome. Stop codon use is also affected by the close proximity of genes; many genes are forced to use TGA and TAG stop codons because they terminate either within the Shine-Dalgarno or coding sequence of the next gene on the chromosome. The implications these results have for the evolution of synonymous codon use are discussed.
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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.