Codon pair optimization (CPO): a software tool for synthetic gene design based on codon pair bias to improve the expression of recombinant proteins in Pichia pastoris

Abstract Background Codon optimization is a common method to improve protein expression levels in Pichia pastoris and the current strategy is to replace rare codons with preferred codons to match the codon usage bias. However, codon-pair contexts have a profound effect on translation efficiency by i...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Yide Huang, Ting Lin, Lingfang Lu, Fan Cai, Jie Lin, Yu′e Jiang, Yao Lin
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Pichia pastoris Codon pair bias Codon pair optimization Synthetic gene design Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/bfca9fcb1ebe40f795be5736a7ce732f
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:bfca9fcb1ebe40f795be5736a7ce732f
record_format	dspace
spelling	oai:doaj.org-article:bfca9fcb1ebe40f795be5736a7ce732f2021-11-08T11:16:09ZCodon pair optimization (CPO): a software tool for synthetic gene design based on codon pair bias to improve the expression of recombinant proteins in Pichia pastoris10.1186/s12934-021-01696-y1475-2859https://doaj.org/article/bfca9fcb1ebe40f795be5736a7ce732f2021-11-01T00:00:00Zhttps://doi.org/10.1186/s12934-021-01696-yhttps://doaj.org/toc/1475-2859Abstract Background Codon optimization is a common method to improve protein expression levels in Pichia pastoris and the current strategy is to replace rare codons with preferred codons to match the codon usage bias. However, codon-pair contexts have a profound effect on translation efficiency by influencing both translational elongation rates and accuracy. Until now, it remains untested whether optimized genes based on codon pair bias results in higher protein expression levels compared to codon usage bias. Results In this study, an algorithm based on dynamic programming was introduced to develop codon pair optimization (CPO) which is a software tool to provide simple and efficient codon pair optimization for synthetic gene design in Pichia pastoris. Two reporters (MT1-MMP E2C6 and ADAM17 A9B8 scFvs) were employed to test the effects of codon pair bias and CPO optimization on their protein expression levels. Four variants of MT1-MMP E2C6 and ADAM17 A9B8 for each were generated, one variant with the best codon-pair context, one with the worst codon-pair context, one with unbiased codon-pair context, and another optimized based on codon usage. The expression levels of variants with the worst codon-pair context were almost undetectable by Western blot and the variants with the best codon-pair context were expressed well. The expression levels on MT1-MMP E2C6 and ADAM17 A9B8 were more than five times and seven times higher in the optimized sequences based on codon-pair context compared to that based on codon usage, respectively. The results indicated that the codon-pair context-based codon optimization is more effective in enhancing expression of protein in Pichia pastoris. Conclusions Codon-pair context plays an important role on the protein expression in Pichia pastoris. The codon pair optimization (CPO) software developed in this study efficiently improved the protein expression levels of exogenous genes in Pichia pastoris, suggesting gene design based on codon pair bias is an alternative strategy for high expression of recombinant proteins in Pichia pastoris.Yide HuangTing LinLingfang LuFan CaiJie LinYu′e JiangYao LinBMCarticlePichia pastorisCodon pair biasCodon pair optimizationSynthetic gene designMicrobiologyQR1-502ENMicrobial Cell Factories, Vol 20, Iss 1, Pp 1-10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Pichia pastoris Codon pair bias Codon pair optimization Synthetic gene design Microbiology QR1-502
spellingShingle	Pichia pastoris Codon pair bias Codon pair optimization Synthetic gene design Microbiology QR1-502 Yide Huang Ting Lin Lingfang Lu Fan Cai Jie Lin Yu′e Jiang Yao Lin Codon pair optimization (CPO): a software tool for synthetic gene design based on codon pair bias to improve the expression of recombinant proteins in Pichia pastoris
description	Abstract Background Codon optimization is a common method to improve protein expression levels in Pichia pastoris and the current strategy is to replace rare codons with preferred codons to match the codon usage bias. However, codon-pair contexts have a profound effect on translation efficiency by influencing both translational elongation rates and accuracy. Until now, it remains untested whether optimized genes based on codon pair bias results in higher protein expression levels compared to codon usage bias. Results In this study, an algorithm based on dynamic programming was introduced to develop codon pair optimization (CPO) which is a software tool to provide simple and efficient codon pair optimization for synthetic gene design in Pichia pastoris. Two reporters (MT1-MMP E2C6 and ADAM17 A9B8 scFvs) were employed to test the effects of codon pair bias and CPO optimization on their protein expression levels. Four variants of MT1-MMP E2C6 and ADAM17 A9B8 for each were generated, one variant with the best codon-pair context, one with the worst codon-pair context, one with unbiased codon-pair context, and another optimized based on codon usage. The expression levels of variants with the worst codon-pair context were almost undetectable by Western blot and the variants with the best codon-pair context were expressed well. The expression levels on MT1-MMP E2C6 and ADAM17 A9B8 were more than five times and seven times higher in the optimized sequences based on codon-pair context compared to that based on codon usage, respectively. The results indicated that the codon-pair context-based codon optimization is more effective in enhancing expression of protein in Pichia pastoris. Conclusions Codon-pair context plays an important role on the protein expression in Pichia pastoris. The codon pair optimization (CPO) software developed in this study efficiently improved the protein expression levels of exogenous genes in Pichia pastoris, suggesting gene design based on codon pair bias is an alternative strategy for high expression of recombinant proteins in Pichia pastoris.
format	article
author	Yide Huang Ting Lin Lingfang Lu Fan Cai Jie Lin Yu′e Jiang Yao Lin
author_facet	Yide Huang Ting Lin Lingfang Lu Fan Cai Jie Lin Yu′e Jiang Yao Lin
author_sort	Yide Huang
title	Codon pair optimization (CPO): a software tool for synthetic gene design based on codon pair bias to improve the expression of recombinant proteins in Pichia pastoris
title_short	Codon pair optimization (CPO): a software tool for synthetic gene design based on codon pair bias to improve the expression of recombinant proteins in Pichia pastoris
title_full	Codon pair optimization (CPO): a software tool for synthetic gene design based on codon pair bias to improve the expression of recombinant proteins in Pichia pastoris
title_fullStr	Codon pair optimization (CPO): a software tool for synthetic gene design based on codon pair bias to improve the expression of recombinant proteins in Pichia pastoris
title_full_unstemmed	Codon pair optimization (CPO): a software tool for synthetic gene design based on codon pair bias to improve the expression of recombinant proteins in Pichia pastoris
title_sort	codon pair optimization (cpo): a software tool for synthetic gene design based on codon pair bias to improve the expression of recombinant proteins in pichia pastoris
publisher	BMC
publishDate	2021
url	https://doaj.org/article/bfca9fcb1ebe40f795be5736a7ce732f
work_keys_str_mv	AT yidehuang codonpairoptimizationcpoasoftwaretoolforsyntheticgenedesignbasedoncodonpairbiastoimprovetheexpressionofrecombinantproteinsinpichiapastoris AT tinglin codonpairoptimizationcpoasoftwaretoolforsyntheticgenedesignbasedoncodonpairbiastoimprovetheexpressionofrecombinantproteinsinpichiapastoris AT lingfanglu codonpairoptimizationcpoasoftwaretoolforsyntheticgenedesignbasedoncodonpairbiastoimprovetheexpressionofrecombinantproteinsinpichiapastoris AT fancai codonpairoptimizationcpoasoftwaretoolforsyntheticgenedesignbasedoncodonpairbiastoimprovetheexpressionofrecombinantproteinsinpichiapastoris AT jielin codonpairoptimizationcpoasoftwaretoolforsyntheticgenedesignbasedoncodonpairbiastoimprovetheexpressionofrecombinantproteinsinpichiapastoris AT yuejiang codonpairoptimizationcpoasoftwaretoolforsyntheticgenedesignbasedoncodonpairbiastoimprovetheexpressionofrecombinantproteinsinpichiapastoris AT yaolin codonpairoptimizationcpoasoftwaretoolforsyntheticgenedesignbasedoncodonpairbiastoimprovetheexpressionofrecombinantproteinsinpichiapastoris
_version_	1718442276793876480

Codon pair optimization (CPO): a software tool for synthetic gene design based on codon pair bias to improve the expression of recombinant proteins in Pichia pastoris

Ejemplares similares