ArticleMicrobial cell factories2024
CRISPR-Cas9 knockout screen informs efficient reduction of the Komagataella phaffii secretome.
Article in Microbial cell factories, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Host-Informed Engineering of Glycosylation in Komagataella phaffii for Human Biantennary N-Linked Glycans.Research square · 2026Article
- Deletion of low-essentiality, secretion-associated genes enhances recombinant protein production in Komagataella phaffii.Microbial cell factories · 2026Article
- Systematic perturbation of cultures of K. phaffii by carbon co-feeding show gene signatures associated with production of recombinant proteins.Microbial cell factories · 2026Article
- Manufacturability is access: redesigning antibody production for equitable pediatric access in LMICs.Frontiers in pediatrics · 2026Article
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Authors and funding
10 authors.
Funding
Abstract
backgroundThe yeast Komagataella phaffii is widely used for manufacturing recombinant proteins, but secreted titers of recombinant proteins could be improved by genetic engineering. In this study, we hypothesized that cellular resources could be redirected from production of endogenous proteins to production of recombinant proteins by deleting unneeded endogenous proteins. In non-model microorganisms such as K. phaffii, however, genetic engineering is limited by lack gene annotation and knowledge of gene essentiality.
resultsWe identified a set of endogenous secreted proteins in K. phaffii by mass spectrometry and signal peptide prediction. Our efforts to disrupt these genes were hindered by limited annotation of essential genes. To predict essential genes, therefore, we designed, transformed, and sequenced a pooled library of guide RNAs for CRISPR-Cas9-mediated knockout of all endogenous secreted proteins. We then used predicted gene essentiality to guide iterative disruptions of up to 11 non-essential genes. Engineered strains exhibited a ~20× increase in the production of human serum albumin and a twofold increase in the production of a monoclonal antibody.
conclusionsWe demonstrated that disruption of as few as six genes can increase production of recombinant proteins. Further reduction of the endogenous proteome of K. phaffii may further improve strain performance. The pooled library of secretome-targeted guides for CRISPR-Cas9 and knowledge of gene essentiality reported here will facilitate future efforts to engineer K. phaffii for production of other recombinant proteins and enzymes.
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