Development of a codon optimization strategy using the efor RED reporter gene as a test case

Chee Hoo Yip, Orr Yarkoni, James Ajioka, Kiew Lian Wan, Sheila Nathan

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Citation (Scopus)

Abstract

Synthetic biology is a platform that enables high-level synthesis of useful products such as pharmaceutically related drugs, bioplastics and green fuels from synthetic DNA constructs. Large-scale expression of these products can be achieved in an industrial compliant host such as Escherichia coli. To maximise the production of recombinant proteins in a heterologous host, the genes of interest are usually codon optimized based on the codon usage of the host. However, the bioinformatics freeware available for standard codon optimization might not be ideal in determining the best sequence for the synthesis of synthetic DNA. Synthesis of incorrect sequences can prove to be a costly error and to avoid this, a codon optimization strategy was developed based on the E. coli codon usage using the efor RED reporter gene as a test case. This strategy replaces codons encoding for serine, leucine, proline and threonine with the most frequently used codons in E. coli. Furthermore, codons encoding for valine and glycine are substituted with the second highly used codons in E. coli. Both the optimized and original efor RED genes were ligated to the pJS209 plasmid backbone using Gibson Assembly and the recombinant DNAs were transformed into E. coli E. cloni 10G strain. The fluorescence intensity per cell density of the optimized sequence was improved by 20% compared to the original sequence. Hence, the developed codon optimization strategy is proposed when designing an optimal sequence for heterologous protein production in E. coli.

Original languageEnglish
Title of host publication2017 UKM FST Postgraduate Colloquium
Subtitle of host publicationProceedings of the University Kebangsaan Malaysia, Faculty of Science and Technology 2017 Postgraduate Colloquium
PublisherAmerican Institute of Physics Inc.
Volume1940
ISBN (Electronic)9780735416321
DOIs
Publication statusPublished - 4 Apr 2018
Event2017 UKM FST Postgraduate Colloquium - Selangor, Malaysia
Duration: 12 Jul 201713 Jul 2017

Other

Other2017 UKM FST Postgraduate Colloquium
CountryMalaysia
CitySelangor
Period12/7/1713/7/17

Fingerprint

genes
deoxyribonucleic acid
optimization
coding
synthesis
proteins
leucine
plasmids
products
glycine
Escherichia
biology
drugs
platforms
assembly
fluorescence
cells

ASJC Scopus subject areas

  • Physics and Astronomy(all)

Cite this

Yip, C. H., Yarkoni, O., Ajioka, J., Wan, K. L., & Nathan, S. (2018). Development of a codon optimization strategy using the efor RED reporter gene as a test case. In 2017 UKM FST Postgraduate Colloquium: Proceedings of the University Kebangsaan Malaysia, Faculty of Science and Technology 2017 Postgraduate Colloquium (Vol. 1940). [020080] American Institute of Physics Inc.. https://doi.org/10.1063/1.5027995

Development of a codon optimization strategy using the efor RED reporter gene as a test case. / Yip, Chee Hoo; Yarkoni, Orr; Ajioka, James; Wan, Kiew Lian; Nathan, Sheila.

2017 UKM FST Postgraduate Colloquium: Proceedings of the University Kebangsaan Malaysia, Faculty of Science and Technology 2017 Postgraduate Colloquium. Vol. 1940 American Institute of Physics Inc., 2018. 020080.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Yip, CH, Yarkoni, O, Ajioka, J, Wan, KL & Nathan, S 2018, Development of a codon optimization strategy using the efor RED reporter gene as a test case. in 2017 UKM FST Postgraduate Colloquium: Proceedings of the University Kebangsaan Malaysia, Faculty of Science and Technology 2017 Postgraduate Colloquium. vol. 1940, 020080, American Institute of Physics Inc., 2017 UKM FST Postgraduate Colloquium, Selangor, Malaysia, 12/7/17. https://doi.org/10.1063/1.5027995
Yip CH, Yarkoni O, Ajioka J, Wan KL, Nathan S. Development of a codon optimization strategy using the efor RED reporter gene as a test case. In 2017 UKM FST Postgraduate Colloquium: Proceedings of the University Kebangsaan Malaysia, Faculty of Science and Technology 2017 Postgraduate Colloquium. Vol. 1940. American Institute of Physics Inc. 2018. 020080 https://doi.org/10.1063/1.5027995
Yip, Chee Hoo ; Yarkoni, Orr ; Ajioka, James ; Wan, Kiew Lian ; Nathan, Sheila. / Development of a codon optimization strategy using the efor RED reporter gene as a test case. 2017 UKM FST Postgraduate Colloquium: Proceedings of the University Kebangsaan Malaysia, Faculty of Science and Technology 2017 Postgraduate Colloquium. Vol. 1940 American Institute of Physics Inc., 2018.
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