The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Precise quantification of translation inhibition by mRNA structures that overlap with the ribosomal footprint in N-terminal coding sequences
Open accessAbstract
A mRNA's translation rate is controlled by several sequence determinants, including the presence of RNA structures within the N-terminal regions of its coding sequences. However, the physical rules that govern when such mRNA structures will inhibit translation remain unclear. Here, we introduced systematically designed RNA hairpins into the N-terminal coding region of a reporter protein with steadily increasing distances from the start codon, followed by characterization of their mRNA and expression levels in Escherichia coli. We found that the mRNAs' translation rates were repressed, by up to 530-fold, when mRNA structures overlapped with the ribosome's footprint. In contrast, when the mRNA structure was located outside the ribosome's footprint, translation was repressed by <2-fold. By combining our measurements with biophysical modeling, we determined that the ribosomal footprint extends 13 nucleotides into the N-terminal coding region and, when a mRNA structure overlaps or partially overlaps with the ribosomal footprint, the free energy to unfold only the overlapping structure controlled the extent of translation repression. Overall, our results provide precise quantification of the rules governing translation initiation at N-terminal coding regions, improving the predictive design of post-transcriptional regulatory elements that regulate translation rate.
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Cites
Coding-Sequence Determinants of Gene Expression in Escherichia coli
Kudla, G., Murray, A. W., Tollervey, D., & Plotkin, J. B. (2009) · Science · doi:10.1126/science.1170160 · Cited by 1,458
The N-end rule: functions, mysteries, uses
Varshavsky, A. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.22.12142 · Cited by 859
Translation efficiency is determined by both codon bias and folding energy
Tuller, T., Waldman, Y. Y., Kupiec, M., & Ruppin, E. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0909910107 · Cited by 584 · cited 1×
“A mRNA’s translation rate is controlled by its sequence through the collective action of several ribosome-mRNA interactions (1-11), creating a complicated sequence-function relationship.”
BackgroundCauses and effects of N-terminal codon bias in bacterial genes
Goodman, D. B., Church, G. M., & Kosuri, S. (2013) · Science · doi:10.1126/science.1241934 · Cited by 573
Permanent genetic memory with >1-byte capacity
Yang, L., Nielsen, A. A. K., Fernandez-Rodriguez, J., McClune, C. J., Laub, M. T., Lu, T. K., & Voigt, C. A. (2014) · Nature Methods · doi:10.1038/nmeth.3147 · Cited by 243
Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria
Farasat, I., Kushwaha, M., Collens, J., Easterbrook, M., Guido, M., & Salis, H. M. (2014) · Molecular Systems Biology · doi:10.15252/msb.20134955 · Cited by 235
Self-citation
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Mustoe, A. M., Busan, S., Rice, G. M., Hajdin, C. E., Peterson, B. K., Ruda, V. M., Kubica, N., Nutiu, R., Baryza, J. L., & Weeks, K. M. (2018) · Cell · doi:10.1016/j.cell.2018.02.034 · Cited by 258
An Automated Model Test System for Systematic Development and Improvement of Gene Expression Models
Reis, A. C., & Salis, H. M. (2020) · ACS Synthetic Biology · doi:10.1021/acssynbio.0c00394 · Cited by 166
Self-citationGeldart, K. G., Kommineni, S., Forbes, M., Hayward, M., Dunny, G. M., Salzman, N. H., & Kaznessis, Y. N. (2018) · Bioengineering & Translational Medicine · doi:10.1002/btm2.10107 · Cited by 93
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
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Metadata
- Authors
- Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., & Salis, H. M.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-02-01
- Volume
- 45
- Issue
- 9
- Pages
- 5437-5448
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- OpenAlex
- W2952214797
- Cited by
- 161
- References
- 6
- FWCI
- 4.76
- Type
- journal article
- Language
- en
- Open access
- gold
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- Espah Borujeni, A., Cetnar, D., Farasat, I., Smith, A., Lundgren, N., & Salis, H. M. (2017). Precise quantification of translation inhibition by mRNA structures that overlap with the ribosomal footprint in N-terminal coding sequences. Nucleic Acids Research. https://doi.org/10.1093/nar/gkx061
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