CRISPR-Cas9 knockout screen informs efficient reduction of the Komagataella phaffii secretome

The yeast Komagataella phaffii is a promising alternative host for manufacturing of therapeutic proteins. Deletion of unneeded endogenous proteins could increase the secreted titer of recombinant proteins by redirecting cellular resources. Genetic engineering in non-model hosts is hampered by limited annotation of genes, especially essential genes. In this study, we identified the set of endogenous secreted proteins in K. phaffii and attempted to disrupt these genes. We designed, transformed, and sequenced a pooled CRISPR-Cas9 knockout library to determine which genes are essential. With this knowledge, we rapidly disrupted up to 9 consecutive genes in K. phaffii. Engineered strains exhibited a ~20x increase in the production of human serum albumin and a 2x increase in the production of a monoclonal antibody. The pooled CRISPR-Cas9 library and knowledge of gene essentiality reported here will facilitate future efforts to engineer K. phaffii for production of other recombinant therapeutic proteins and enzymes. Overall design: This experiment is a head to head comparison of the transcriptomes of two yeast strains. The strains are compared during expression of two proteins, human serum albumin (HSA) and trastuzumab.