Improvement of DNA minicircle production by optimization of the secondary structure of the 5′-UTR of ParA resolvase
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Author(s)
Brito, Liliana
Alves, Cláudia P. A.
Monteiro, Gabriel A.
Simcikova, Michaela
Jones, Kristala L
Prazeres, Duarte Miguel
Jones, Kristala L.
Date Issued
May 2016
Journal
Applied Microbiology and Biotechnology
Publisher
Springer Berlin Heidelberg
Citation
Šimčíková, Michaela et al. “Improvement of DNA Minicircle Production by Optimization of the Secondary Structure of the 5′-UTR of ParA Resolvase.” Applied Microbiology and Biotechnology 100.15 (2016): 6725–6737.
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Author's final manuscript
Abstract
The use of minicircles in gene therapy applications is dependent on the availability of high-producer cell systems. In order to improve the performance of minicircle production in Escherichia coli by ParA resolvase-mediated in vivo recombination, we focus on the 5′ untranslated region (5′-UTR) of parA messenger RNA (mRNA). The arabinose-inducible P[subscript BAD]/araC promoter controls ParA expression and strains with improved arabinose uptake are used. The 27-nucleotide-long 5′-UTR of parA mRNA was optimized using a predictive thermodynamic model. An analysis of original and optimized mRNA subsequences predicted a decrease of 8.6–14.9 kcal/mol in the change in Gibbs free energy upon assembly of the 30S ribosome complex with the mRNA subsequences, indicating a more stable mRNA-rRNA complex and enabling a higher (48–817-fold) translation initiation rate. No effect of the 5′-UTR was detected when ParA was expressed from a low-copy number plasmid (∼14 copies/cell), with full recombination obtained within 2 h. However, when the parA gene was inserted in the bacterial chromosome, a faster and more effective recombination was obtained with the optimized 5′-UTR. Interestingly, the amount of this transcript was 2.6–3-fold higher when compared with the transcript generated from the original sequence, highlighting that 5′-UTR affects the level of the transcript. A Western blot analysis confirmed that E. coli synthesized higher amounts of ParA with the new 5′-UTR (∼1.8 ± 0.7-fold). Overall, these results show that the improvements made in the 5′-UTR can lead to a more efficient translation and hence to faster and more efficient minicircle generation.
MIT Department
MIT-Portugal Program
Massachusetts Institute of Technology. Department of Chemical Engineering
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DOI of Published Version
https://doi.org/10.1007/s00253-016-7565-x
