The advent of protein-based therapeutics has led to an increased need for large scale production of recombinant proteins. One of the widely used yeast species for commercial protein production is Pichia pastoris. Protein production using eukaryotes such as yeast allows proper disulfide bond formation and glycosylation, which is not possible in bacteria such as E.coli. Additionally, Pichia pastoris has several advantages over the yeast S. cerevisiae for protein production including growth in minimal medium, the ability to use methanol as a carbon source, and the ability to grow at very high density, all of which lead to more efficient protein production. However, the molecular toolkit for Pichia pastoris has lagged significantly behind those available in E.coli and S. cerevisiae. The inventors of this technology have expanded the Pichia pastoris toolkit to include recombinase-based site-specific genome engineering and an inducible expression system to drive high levels of recombinant protein expression.