ArticleNucleic acids research2000
Gradients in nucleotide and codon usage along Escherichia coli genes.
Article in Nucleic acids research, 2000. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Efficient genetic code expansion without host genome modifications.Nature biotechnology · 2025Article
- Comparative genomics of thermosynechococcaceae and thermostichaceae: insights into codon usage bias.Acta biochimica Polonica · 2024Article
- Codon usage bias in yeasts and its correlation with gene expression, growth temperature, and protein structure.Frontiers in microbiology · 2024Article
- Benchmarking Community-Wide Estimates of Growth Potential from Metagenomes Using Codon Usage Statistics.mSystems · 2022Article
- Codon usage bias and environmental adaptation in microbial organisms.Molecular genetics and genomics : MGG · 2021Article
- Estimating maximal microbial growth rates from cultures, metagenomes, and single cells via codon usage patterns.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- The complete chloroplast genome of Stauntonia chinensis and compared analysis revealed adaptive evolution of subfamily Lardizabaloideae species in China.BMC genomics · 2021Article
- Evolutionary selection against short nucleotide sequences in viruses and their related hosts.DNA research : an international journal for rapid publication of reports on genes and genomes · 2020Article
- Codon usage analysis of photolyase encoding genes of cyanobacteria inhabiting diverse habitats.3 Biotech · 2017Article
- A deterministic mathematical model for bidirectional excluded flow with Langmuir kinetics.PloS one · 2017Article
- Nucleotide diversity analysis highlights functionally important genomic regions.Scientific reports · 2016Article
- Emergent rules for codon choice elucidated by editing rare arginine codons in Escherichia coli.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Quantitative assessment of ribosome drop-off in E. coli.Nucleic acids research · 2016Article
- Codon usage and codon context bias in Xanthophyllomyces dendrorhous.BMC genomics · 2015Article
- Gaining insights into the codon usage patterns of TP53 gene across eight mammalian species.PloS one · 2015Article
- A cross talk between codon usage bias in human oncogenes.Bioinformation · 2014Article
- Characterization of synonymous codon usage bias in the pseudorabies virus US1 gene.Virologica Sinica · 2012Article
- Mapping codon usage of the translation initiation region in porcine reproductive and respiratory syndrome virus genome.Virology journal · 2011Article
- Interspecific and intragenic differences in codon usage bias among vertebrate myosin heavy-chain genes.Journal of molecular evolution · 2011Article
- GC3 biology in corn, rice, sorghum and other grasses.BMC genomics · 2010Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The usage of codons and nucleotide combinations varies along genes and systematic variation causes gradients in usage. We have studied such gradients of nucleotides and nucleotide combinations and their immediate context in Escherichia coli. To distinguish mutational and selectional effects, the genes were subdivided into three groups with different codon usage bias and the gradients of nucleotide usage were studied in each group. Some combinations that can be associated with a propensity for processivity errors show strong negative gradients that become weaker in genes with low codon bias, consistent with a selection on translational efficiency. One of the strongest gradients is for third position G, which shows a pervasive positive gradient in usage in most contexts of surrounding bases.
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