Yeasts provide an excellent expression system that shares the prokaryotes' potential for large-scale culture thanks to cheap and simple incubation conditions.

A yeast expression system can be a fast and economical way of producing recombinant proteins. Yeast has a short generation time and is easy to grow and scale up in simple media. It can be used for the expression of intracellular or secreted proteins. Since yeast is a eukaryotic cell, yeast expression avoids many of the post-translational and folding problems that are sometimes found in bacterial expression systems. And of course the protein is free of bacterial endotoxins.

Pichia pastoris is a popular yeast strain for recombinant expression. This strain has the ability to use methanol as a carbon source. Protein expression can be induced using the alcohol oxidase 1 (AOX1) promoter. Another advantage of P. pastoris is that it avoids the hyper-glycosylation of proteins that can occur when expressed in Saccharomyces cerevisiae.

Proteins can be expressed either internally or secreted. The gene can be cloned into an expression vector downstream from the α-factor secretion signal for secretion into the media. Pichia secretes very low levels of its own proteins, so a secreted heterologous protein is easy to purify. However, internal expression might be preferable for proteins which are large or contain hydrophobic regions.

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