The quest for the best cell factory for recombinant protein production: Yarrowia lipolytica vs Pichia pastoris

In the present study, the performances of the emerging cell factories Y. lipolytica and P. pastoris were compared for their ability to synthetize and secrete recombinant proteins in bioreactors. As a case study, the lipase CalB from Candida antarctica was cloned under the control of the strong inducible promoters pEYK300A3B and pAOX1 and expressed in Y. lipolytica EYK1ko and P. pastoris MutS recipient strains, respectively. Surprisingly, Y. lipolytica performances were far superior in terms of cell growth, extracellular lipase activity, although P. pastoris showed a significantly higher level of CalB gene expression. According to our results, neither of codon usage bias, protein processing and secretion, or CalB lipase inactivation could be incriminated. It is therefore hypothesized that the observed difference lies in post-translational mechanisms activated by the overexpression of recombinant proteins, namely the unfolded protein response (UPR) and the endoplasmic reticulum (ER) associated degradation (ERAD). Here indeed, the proteasome was shown activated in P. pastoris following recombinant protein expression. In conclusion, keeping specific process constraints in mind, the selection of the adequate cell factory can dramatically improve the production of a given recombinant protein.