Predictive design of mRNA translation initiation region to control prokaryotic translation efficiency
Open accessAbstract
Precise prediction of prokaryotic translation efficiency can provide valuable information for optimizing bacterial host for the production of biochemical compounds or recombinant proteins. However, dynamic changes in mRNA folding throughout translation make it difficult to assess translation efficiency. Here, we systematically determined the universal folding regions that significantly affect the efficiency of translation in Escherichia coli. By assessing the specific regions for mRNA folding, we could construct a predictive design method, UTR Designer, and demonstrate that proper codon optimization around the 5'-proximal coding sequence is necessary to achieve a broad range of expression levels. Finally, we applied our method to control the threshold value of input signals switching on a genetic circuit. This should increase our understanding of the processes underlying gene expression and provide an efficient design principle for optimizing various biological systems, thereby facilitating future efforts in metabolic engineering and synthetic biology.
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A fully rational approach to designing functional 5′ UTRs has not yet been implemented.
“While there has been some success in this effort in prokaryotes, yeast and even mammalian cells27,34–36, a fully rational approach to designing functional 5′ UTRs has not yet been implemented.”
From Human 5′ UTR design and variant effect prediction from a massively parallel translation assay (2019) · cites this paper as [34]
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Dual UTR-A novel 5′ untranslated region design for synthetic biology applications
Balzer Le, S., Onsager, I., Lorentzen, J. A., & Lale, R. (2020) · Synthetic Biology · doi:10.1093/synbio/ysaa006 · Cited by 22 · see citing works
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- Authors
- Seo, S. W., Yang, J.-S., Kim, I., Yang, J., Min, B. E., Kim, S., & Jung, G. Y.
- Affiliations
- Pohang University of Science and Technology (KR)
- Corresponding author
- Kim, Sanguk
- Jung, Gyoo Yeol
- Venue
- Metabolic Engineering
- Publisher
- Elsevier BV
- Published
- 2013-01
- Volume
- 15
- Pages
- 67-74
- ISSN
- 1096-7176 (ISSN-L)
- OpenAlex
- W2020366340
- Cited by
- 300
- References
- 2
- Citations by year
- 2026: 22 · 2025: 22 · 2024: 31 · 2023: 18 · 2022: 28 · 2021: 25 · 2020: 31 · 2019: 19 · 2018: 18 · 2017: 27 · 2016: 27 · 2015: 13 · 2014: 13 · 2013: 4 · 2012: 2
- FWCI
- 3.85
- Type
- journal article
- Language
- en
- Open access
- green
- hdl.handle.net
- Licence
- Locations
- Metabolic Engineering (publishedVersion)
- PubMed (publishedVersion)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion, cc-by-nc-nd)
- Open Access System for Information Sharing (Pohang University of Science and Technology) (submittedVersion)
- Funders
- National Research Foundation
- National Research Foundation of Korea (ABC-2010-0029800)
- Ministry of Education, Science and Technology (ABC-2010–0029800, R31-2010-000-10100-0)
- Ministry of Land, Transport and Maritime Affairs
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Keywords
- mRNA translation efficiency, prokaryotic translation, mRNA folding, 5' untranslated region, codon optimization, Escherichia coli, synthetic gene circuits, gene expression regulation, synthetic biology
- MeSH terms
- Algorithms, Base Sequence, Computer Simulation, Escherichia coli, Models, Genetic, Molecular Sequence Data, Peptide Chain Initiation, Translational, RNA, Messenger, Protein Engineering, Gene Expression Regulation, Bacterial
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