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Expression efficiency and sequence-based factors: a comparative view on 79 human genes in Pichia pastoris

High yield expression of heterologous proteins is usually a matter of "trial and error". In the search of parameters with a major impact on expression, we have applied a comparative analysis to 79 homologous strains of Pichia pastoris harbouring different human cDNAs. Recombinant protein expression was monitored in a standardized procedure and classified with respect to the expression level. More than ten sequence-based parameters with a possible influence on the expression level were analysed. Three factors proved to have a statistically significant association with the expression level. Low abundance of AT-rich regions in the cDNA associates with a high expression level, indicating that correct transcript processing is a major determinant for the expression success in this yeast. A comparatively high isoelectric point of the recombinant protein associates with failure of expression and, finally, the occurrence of a protein homologue in yeast is associated with detectable protein expression. Interestingly, some often discussed factors like codon usage or GC content did not show a significant impact on protein yield.

These results could provide a basis for a knowledge-oriented optimisation of gene sequences both to increase protein yields and to help target selection and the design of high-throughput expression approaches.

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Correspondence to Mewes Böttner.

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Open Access This article is published under license to BioMed Central Ltd. This is an Open Access article is distributed under the terms of the Creative Commons Attribution 2.0 International License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Lang, C., Böttner, M. Expression efficiency and sequence-based factors: a comparative view on 79 human genes in Pichia pastoris. Microb Cell Fact 5, S34 (2006).

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  • Recombinant Protein
  • Codon Usage
  • Heterologous Protein
  • Pichia Pastoris
  • Protein Yield