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Nonrandom utilization of codon pairs in Escherichia coli.
Open accessAbstract
We have analyzed protein-coding sequences of Escherichia coli and find that codon-pair utilization is highly biased, reflecting overrepresentation or underrepresentation of many pairs compared with their random expectations. This effect is over and above that contributed by nonrandomness in the use of amino acid pairs, which itself is highly evident; it is much weaker when nonadjacent codon pairs are examined and virtually disappears when pairs separated by two or three intervening codons are evaluated. There appears to be a high degree of directionality in this bias: any codon that participates in many nonrandom pairs tends to make both over- and underrepresented pairs, but preferentially as a left- or right-hand member. We show a relationship between codon-pair utilization patterns and levels of gene expression: genes encoding proteins expressed at high levels tend to contain more abundant, but more highly underrepresented, codon pairs, relative to genes expressed at low levels. The nonrandom utilization of codon pairs may be a consequence of their effects on translational efficiency, which in turn may be related to the compatibility of adjacent aminoacyl-tRNA isoacceptors at the A and P sites of a translating ribosome.
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Bifunctional enhancement of a β-glucanase-xylanase fusion enzyme by optimization of peptide linkers
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“Although the reasons are still not well understood, some codon pairs occur more frequently, and others less frequently, than expected [12].”
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Synonymous Virus Genome Recoding as a Tool to Impact Viral Fitness
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BackgroundZika Virus Attenuation by Codon Pair Deoptimization Induces Sterilizing Immunity in Mouse Models
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“88 Codon pair bias is interpreted as the unequal frequency in the usage of synonymous 89 codon pairs in certain species (27-29).”
BackgroundThe translational termination signal database
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“It is known that, among the synonymous codon pairs encoding the same amino acid residues, some codon pairs occur more frequently than others in certain species (Fedorov et al., 2002; Gutman and Hatfield, 1989; Moura et al., 2007), which is known as codon-pair bias.”
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“Here, we report attempts to develop a live attenuated VSV strain, making use of a genetic phenomenon known as codon pair bias (CPB) (15, 16).”
MethodPhysical and genetic map of the Neisseria gonorrhoeae strain MS11‐N198 chromosome
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Bicodon bias can determine the role of synonymous SNPs in human diseases
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“In addition, we have also computed the residual score χ2, defined in [42], which indicates when the observed bicodon bias can be explained, or not, by the codon usage bias.”
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RNA stem-loop enhanced expression of previously non-expressible genes
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“CPB is observed across the kingdoms of life, can be quantified statistically [1, 2], and”
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MethodGenetic Engineering of Polymeric Materials
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Trimpert, J., Adler, J. M., Eschke, K., Abdelgawad, A., Firsching, T. C., Ebert, N., Thao, T. T. N., Gruber, A. D., Thiel, V., Osterrieder, N., et al. (2021) · Science Advances · doi:10.1126/sciadv.abk0172 · Cited by 41
“CPD is based on the observation that some codon pairs occur in protein-coding sequences significantly less or more frequently than would be statistically expected (26).”
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Gao, L., Wang, L., Huang, C., Yang, L., Guo, X.-K., Yu, Z., Liu, Y., Yang, P., & Feng, W.-H. (2015) · Virology · doi:10.1016/j.virol.2015.07.012 · Cited by 40
“This phenomenon is termed as codon pair bias (CPB) (Gutman and Hatfield, 1989).”
BackgroundHuman body temperature and new approaches to constructing temperature-sensitive bacterial vaccines
White, M. D., Bosio, C. M., Duplantis, B. N., & Nano, F. E. (2011) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-011-0734-2 · Cited by 39
“Also, changes in the nucleotide sequence could affect the efficiency of translation if rare codons [75, 76] or rare codon pairs [77] for the host organism are introduced.”
Species-Specific Codon Context Rules Unveil Non-Neutrality Effects of Synonymous Mutations
Moura, G. R., Pinheiro, M. M., Freitas, A. V., Oliveira, J. L., Frommlet, J. C., Carreto, L. C., Soares, A. R., Bezerra, A. R., & Santos, M. A. S. (2011) · PLoS ONE · doi:10.1371/journal.pone.0026817 · Cited by 39
“independent of codon-usage biases [3,4], indicating that these two”
BackgroundPicataggio, S. K. (2009) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2009.04.003 · Cited by 39
Codon usage and codon context bias in Xanthophyllomyces dendrorhous
Baeza, M., Alcaı́no, J., Barahona, S., Sepúlveda, D., & Cifuentes, V. (2015) · BMC Genomics · doi:10.1186/s12864-015-1493-5 · Cited by 39
“Codon context bias is likely associated with the accuracy of decoding, indicating the ability of the translational machinery to detect codon pairs present at ribosomal decoding sites [30-33].”
BackgroundFages‐Lartaud, M., Hundvin, K., & Hohmann‐Marriott, M. F. (2022) · The Plant Journal · doi:10.1111/tpj.15970 · Cited by 41
“The expected codon pair frequency ( e ij ) was corrected for the dipeptide bias as previously described (Buchan et al., 2006; Gutman & Hatfield, 1989).”
InfluentialIn silico methods for predicting functional synonymous variants
Lin, B. C., Katneni, U., Jankowska, K. I., Meyer, D., & Kimchi‐Sarfaty, C. (2023) · Genome biology · doi:10.1186/s13059-023-02966-1 · Cited by 41
Shao, Z., Zhang, Y., Feng, X.-Y., Wang, B., & Chen, J. (2012) · PLoS ONE · doi:10.1371/journal.pone.0033547 · Cited by 38
“It has been found that adjacent codon pairs, which encode either the same or different amino acids, have biased occurrence frequencies within a genome [24,25].”
BackgroundDifferential bicodon usage in lowly and highly abundant proteins
Diambra, L. A. (2017) · PeerJ · doi:10.7717/peerj.3081 · Cited by 37
“has been previously established in (Gutman and Hatfield, 1989; Buchan et al., 2006).”
BackgroundMethodResultInfluentialBuckingham, R. H. (1990) · Cellular and Molecular Life Sciences · doi:10.1007/bf01936922 · Cited by 39
TISIGNER.com: web services for improving recombinant protein production
Bhandari, B. K., Lim, C. S., & Gardner, P. P. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab175 · Cited by 38
Attenuation of Human Respiratory Viruses by Synonymous Genome Recoding
Nouën, C. L., Collins, P. L., & Buchholz, U. J. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2019.01250 · Cited by 39
“These Leu and Ser mutations did not affect the CB, CPB, CpG content or dinucleotide frequency ( Figure 1D ) (15).”
BackgroundMethodInfluentialUnderstanding the Genetic Code
Saier, M. H. (2019) · Journal of Bacteriology · doi:10.1128/jb.00091-19 · Cited by 44
Can simple codon pair usage predict protein–protein interaction?
Zhou, Y., Zhou, Y., He, F., Song, J., & Zhang, Z. (2012) · Molecular BioSystems · doi:10.1039/c2mb05427b · Cited by 38
Codon engineering for improved antibody expression in mammalian cells
Carton, J. M., Sauerwald, T. M., Hawley‐Nelson, P., Morse, B. A., Peffer, N. J., Beck, H., Lu, J., Cotty, A., Amegadzie, B. Y., & Sweet, R. (2007) · Protein Expression and Purification · doi:10.1016/j.pep.2007.05.017 · Cited by 34
Spatial Patterns of Gene Expression in Bacterial Genomes
Lato, D. F., & Golding, G. B. (2020) · Journal of Molecular Evolution · doi:10.1007/s00239-020-09951-3 · Cited by 31
Metadata
- Authors
- Gutman, G. A., & Hatfield, G. W.
- Affiliations
- University of California, Irvine (US)
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 1989-05
- Volume
- 86
- Issue
- 10
- Pages
- 3699-3703
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC287207
- OpenAlex
- W2063504601
- Semantic Scholar
- 2e078282edbdc0cc228e53846cc1e546a9101d97
- Cited by
- 261
- References
- 38
- Citations by year
- 2026: 4 · 2025: 1 · 2024: 6 · 2023: 6 · 2022: 9 · 2021: 16 · 2020: 14 · 2019: 16 · 2018: 8 · 2017: 17 · 2016: 11 · 2015: 14 · 2014: 11 · 2013: 7 · 2012: 12
- FWCI
- 2.73
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (submittedVersion)
- Funders
- University of Southern California
- U.S. Public Health Service
- University of California, San Diego
- National Institute of General Medical Sciences (GM24330)
- National Institute of Allergy and Infectious Diseases (AI-21366)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- codon pair bias, Escherichia coli, gene expression levels, translation efficiency, protein-coding sequences, codon usage
- MeSH terms
- Bacterial Proteins, Codon, DNA, Bacterial, Escherichia coli, Gene Expression Regulation, Genes, Bacterial, Peptide Chain Termination, Translational, Probability, RNA, Messenger
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