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Background  Recombinant human granulocyte-macrophage colony-stimulating factor (rhGM-CSF) is a glycoprotein that has been approved by the FDA for the treatment of neutropenia and leukemia in combination with chemotherapies. Recombinant hGM-CSF is produced industrially using the baker’s yeast,  Saccharomyces cerevisiae , by large-scale fermentation. The methylotrophic yeast,  Pichia pastoris , has emerged as an alternative host cell system due to its shorter and less immunogenic glycosylation pattern together with higher cell density growth and higher secreted protein yield than  S. cerevisiae . In this study, we compared the pipeline from gene to recombinant protein in these two yeasts.    Results  Codon optimization  in silico  for both yeast species showed no difference in frequent codon usage. However, rhGM-CSF expressed from  S. cerevisiae  BY4742 showed a significant discrepancy in molecular weight from those of  P. pastoris  X33. Analysis showed purified rhGM-CSF species with molecular weights ranging from 30 to more than 60 kDa. Fed-batch fermentation over 72 h showed that rhGM-CSF was more highly secreted from  P. pastoris  than  S. cerevisiae  (285 and 64 mg total secreted protein/L, respectively). Ion exchange chromatography gave higher purity and recovery than hydrophobic interaction chromatography. Purified rhGM-CSF from  P. pastoris  was 327 times more potent than rhGM-CSF from  S. cerevisiae  in terms of proliferative stimulating capacity on the hGM-CSF-dependent cell line, TF-1.    Conclusion  Our data support a view that the methylotrophic yeast  P. pastoris  is an effective recombinant host for heterologous rhGM-CSF production.    Electronic supplementary material  The online version of this article (doi:10.1186/s13104-017-2471-6) contains supplementary material, which is available to authorized users.

Pichia pastoris versus Saccharomyces cerevisiae: a case study on the recombinant production of human granulocyte-macrophage colony-stimulating factor