Codon Pair Utilization Biases Influence Translational Elongation Step Times
Open accessAbstract
Two independent assays capable of measuring the relative in vivo translational step times across a selected codon pair in a growing polypeptide in the bacterium Escherichia coli have been employed to demonstrate that codon pairs observed in protein coding sequences more frequently than predicted (over-represented codon pairs) are translated slower than pairs observed less frequently than expected (under-represented codon pairs). These results are consistent with the findings that translational step times are influenced by codon context and that these context effects are related to the compatabilities of adjacent tRNA isoacceptor molecules on the surface of a translating ribosome. These results also support our previous suggestion that the frequency of one codon next to another has co-evolved with the structure and abundance of tRNA isoacceptors in order to control the rates of translational step times without imposing additional constraints on amino acid sequences or protein structures.
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Codon context is more strongly related to translational efficiency than single codon usage.
“Moreover, experimental results support the observation that codon context is more strongly related to translational efficiency than single codon usage [1].”
From Preferred and avoided codon pairs in three domains of life (2008) · cites this paper as [1]
Effects of codon context are influenced by physical interactions between tRNA isoacceptors in the ribosomal P- and A-sites.
“Previous studies suggest that the effects of codon context are influenced by the physical interactions between tRNA isoacceptors in the ribosomal P- and A-sites [1,16,23].”
From Preferred and avoided codon pairs in three domains of life (2008) · cites this paper as [1]
Codon context can influence translational elongation rates.
“It is suggested that codon context biases are associated with translational efficiency, since codon context influences translational elongation rates [1].”
From Preferred and avoided codon pairs in three domains of life (2008) · cites this paper as [1]
Codon context is even more important than single codon usage for translational efficiency.
“It has been proposed that codon context is even more important than single codon usage for translational efficiency [1].”
From Preferred and avoided codon pairs in three domains of life (2008) · cites this paper as [1]
Codon context is even more important than codon usage for translational efficiency.
“It has been proposed that codon context is even more important than codon usage for translational efficiency [1].”
From Preferred and avoided codon pairs in three domains of life (2008) · cites this paper as [1]
Codon context might be influenced by certain structural constraints imposed by two tRNAs occupying the ribosomal P- and A-sites.
“In addition, it has been suggested that codon context might be influenced by certain structural constraints imposed by two tRNAs occupying the ribosomal P- and A-sites [1,16,23].”
From Preferred and avoided codon pairs in three domains of life (2008) · cites this paper as [1]
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Cites
Nonrandom utilization of codon pairs in Escherichia coli.
Gutman, G. A., & Hatfield, G. W. (1989) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.86.10.3699 · Cited by 261 · cited 6× · see citing works
“Since our previous statistical analyses (Gutman and Hatfield, 1989; Hatfield and Gutman, 1992) showed that there is no correlation between the directionality of a codon pair and its bias, i.e. codon pair A-B versus B-A, we also wished to determine if there is a lack of correlation between the…”
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Research works printed but not linked: 10
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Ingolia, N. T., Lareau, L. F., & Weissman, J. S. (2011) · Cell · doi:10.1016/j.cell.2011.10.002 · Cited by 2,187 · see citing works
Preferred and avoided codon pairs in three domains of life
Tats, A., Tenson, T., & Remm, M. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-463 · Cited by 112 · see citing works
“We observed only one conserved 1–3 interaction, over-representation of the pattern GGUnnnGGU, indicating that interactions between the ribosomal E- and A-sites do not influence the codon context as much as interactions between the P- and A-sites.”
BackgroundResultInfluentialMoura, G., Pinheiro, M., Arrais, J., Gomes, A. C., Carreto, L., Freitas, A., Oliveira, J. L., & Santos, M. A. S. (2007) · PLoS ONE · doi:10.1371/journal.pone.0000847 · Cited by 107 · see citing works
Comparative context analysis of codon pairs on an ORFeome scale
Moura, G., Pinheiro, M., Silva, R., Miranda, I., Afreixo, V., Dias, G., Freitas, A., Oliveira, J. L., & Santos, M. A. (2005) · Genome Biology · doi:10.1186/gb-2005-6-3-r28 · Cited by 90 · see citing works
Alexaki, A., Hettiarachchi, G. K., Athey, J. C., Katneni, U. K., Simhadri, V., Hamasaki-Katagiri, N., Nanavaty, P., Lin, B., Takeda, K., Freedberg, D., et al. (2019) · Scientific Reports · doi:10.1038/s41598-019-51984-2 · Cited by 78 · see citing works
A relationship between mRNA expression levels and protein solubility in E. coli
Tartaglia, G. G., Pechmann, S., Dobson, C. M., & Vendruscolo, M. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.03.002 · Cited by 63 · see citing works
Codon-triplet context unveils unique features of the Candida albicans protein coding genome
Moura, G. R., Lousado, J. P., Pinheiro, M., Carreto, L., Silva, R. M., Oliveira, J. L., & Santos, M. A. (2007) · BMC Genomics · doi:10.1186/1471-2164-8-444 · Cited by 9 · see citing works
- Authors
- Irwin, B., Heck, J. D., & Hatfield, G. W.
- Affiliations
- University of California, Irvine (US)
- Corresponding author
- Hatfield, G. Wesley
- Venue
- Journal of Biological Chemistry
- Publisher
- Elsevier BV
- Published
- 1995-09
- Volume
- 270
- Issue
- 39
- Pages
- 22801-22806
- ISSN
- 0021-9258 (ISSN-L)
- OpenAlex
- W2125076649
- Cited by
- 166
- References
- 1
- Citations by year
- 2026: 2 · 2025: 4 · 2024: 2 · 2023: 6 · 2022: 4 · 2021: 10 · 2020: 4 · 2019: 4 · 2018: 3 · 2017: 7 · 2016: 8 · 2015: 10 · 2014: 8 · 2013: 5 · 2012: 16
- FWCI
- 0.98
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Journal of Biological Chemistry (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health (5r01gm049388-04)
- National Institute of General Medical Sciences (GM 49388)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Keywords
- codon pair bias, translation elongation, codon context, tRNA isoacceptors, ribosome, translation speed, codon usage, Escherichia coli
- MeSH terms
- Amino Acid Sequence, Base Composition, beta-Galactosidase, Codon, Escherichia coli, Genes, Bacterial, Kinetics, Molecular Sequence Data, Operon, Peptide Chain Elongation, Translational, Plasmids, Recombinant Fusion Proteins, Ribosomes, RNA, Transfer, Amino Acid-Specific, RNA, Transfer, Trp, Species Specificity, Transcription, Genetic, Protein Biosynthesis, Tryptophan
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