Evidence map›Paper›PMID 42116141›Full record

ArticleMicrobial cell factories2026

Deletion of low-essentiality, secretion-associated genes enhances recombinant protein production in Komagataella phaffii.

Hayley Ford, Neil C Dalvie, Timothy R Lorgeree, Rachel M Barry, Anaisa N Sibel, Rachel A Ahlmark, Harini Narayanan, Brittney C Sunday, Charles A Whittaker, Raghav Acharya and 2 more

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Article in Microbial cell factories, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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1 · What the graph read from it

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2 · The registry

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3 · Its place in the literature

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4 · The record

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5 · Who and what money

Authors and funding

12 authors.

Hayley FordDepartment of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139, USA.ORCID http://orcid.org/0000-0002-2586-8178
Neil C DalvieDepartment of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139, USA.
Timothy R LorgereeKoch Institute for Integrative Cancer Research at MIT, 500 Main Street, MA, 02139, Cambridge, USA.
Rachel M BarryKoch Institute for Integrative Cancer Research at MIT, 500 Main Street, MA, 02139, Cambridge, USA.
Anaisa N SibelDepartment of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139, USA.
Rachel A AhlmarkDepartment of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139, USA.
Harini NarayananKoch Institute for Integrative Cancer Research at MIT, 500 Main Street, MA, 02139, Cambridge, USA.
Brittney C SundayDepartment of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139, USA.
Charles A WhittakerKoch Institute for Integrative Cancer Research at MIT, 500 Main Street, MA, 02139, Cambridge, USA.
Raghav AcharyaDepartment of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139, USA.
Carmen M ElenbergerKoch Institute for Integrative Cancer Research at MIT, 500 Main Street, MA, 02139, Cambridge, USA.
J Christopher LoveDepartment of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, 02139, USA. clove@mit.edu.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundKomagataella phaffii (K. phaffii) is used to manufacture biologic medicines, food proteins, reagents, and materials. Despite its increasing prevalence, further improvements to its productivity would enhance its economic and operational benefits. Genomic engineering represents one approach to increase its cell-specific productivity. We hypothesized that combining the metrics for the relative essentiality of genes with biological inference for relevance to protein secretion could identify genes that, when disrupted, would improve specific productivity in the resulting strains.

resultsThe essentiality of genes in K. phaffii (NRRL Y-11430) were predicted through a genome-wide knockout screen using CRISPR-Cas9. Based on the results from this screen, we selected and subsequently disrupted the least essential genes from two gene groups heavily associated with secretion, namely those relating to the cell wall and vacuolar transport. Strains of K. phaffii with single gene disruptions from these gene sets showed significantly improved production of a monoclonal antibody (mAb). These strains exhibited no discernible differences in growth or apparent profiles of host cell proteins when compared to the parental strain. The best-performing strains consistently showed 2-3x enhancements in specific productivity and titers across scales (3-150 mL), culture formats (plates, flasks, bioreactors), and processing operations (batch and fed-batch).

conclusionsThis study demonstrates how combining data on gene essentiality and prior knowledge of biological pathways related to a phenotypic trait of interest (here protein secretion) can inform strain engineering to enhance the trait. This study expands the catalog of genetically engineered strains of K. phaffii with improved productivity. These strains support the long-term goal of achieving low-cost, high-volume production of recombinant proteins using this host. Further engineering of these strains and optimization of fermentation processes could enable volumetric productivities comparable to those of other established hosts used to produce mAbs and other complex recombinant proteins.

Indexed as

Gene DeletionGenes, EssentialRecombinant ProteinsSaccharomycetalesAntibodies, MonoclonalCRISPR-Cas SystemsAntibodies, MonoclonalRecombinant Proteinsalternative hostCRISPR/Cas9genome-wide screenPichia pastoris

Identifiers

PMID42116141
PMCPMC13343958

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