Abstract
Komagataella phaffii, also known as Pichia pastoris, is a common host for the production of biologics and enzymes, due to fast growth, high productivity, and advancements in host engineering. Several K. phaffii variants are commonly used as interchangeable base strains, which confounds efforts to improve this host. In this study, genomic and transcriptomic analyses of Y‐11430 (CBS7435), GS115, X‐33, and eight other variants enabled a comparative assessment of the relative fitness of these hosts for recombinant protein expression. Cell wall integrity explained the majority of the variation among strains, impacting transformation efficiency, growth, methanol metabolism, and secretion of heterologous proteins. Y‐11430 exhibited the highest activity of genes involved in methanol utilization, up to two‐fold higher transcription of heterologous genes, and robust growth. With a more permeable cell wall, X‐33 displayed a six‐fold higher transformation efficiency and up to 1.2‐fold higher titers than Y‐11430. X‐33 also shared nearly all mutations, and a defective variant of HIS4, with GS115, precluding robust growth. Transferring two beneficial mutations identified in X‐33 into Y‐11430 resulted in an optimized base strain that provided up to four‐fold higher transformation efficiency and three‐fold higher protein titers, while retaining robust growth. The approach employed here to assess unique banked variants in a species and then transfer key beneficial variants into a base strain should also facilitate rational assessment of a broad set of other recombinant hosts.
Highlights
Pipelines for recombinant biopharmaceuticals include a growing number of forms and structures, including single‐domain antibodies, fusion proteins, antibody‐drug conjugates, bi‐specific antibodies, and subunit vaccines
K. phaffii Y‐11430 was mutagenized with nitrosoguanidine to generate the histidine auxotroph, GS115, which became popular for the ease of integrating a heterologous gene into the genome using complementation of HIS4 (Cregg, 1989; Cregg, Barringer, Hessler, & Madden, 1985; De Schutter et al, 2009)
Our analyses revealed the integrity of the cell wall likely confers the largest source of variation in performance among these strains
Summary
Pipelines for recombinant biopharmaceuticals include a growing number of forms and structures, including single‐domain antibodies, fusion proteins, antibody‐drug conjugates, bi‐specific antibodies, and subunit vaccines This increasing diversity, coupled with increasing global demand for such products at reduced costs, present certain challenges for the host organisms commonly used today for production (Legastelois et al, 2017; Matthews et al, 2017). A framework for the rational evaluation of potential hosts could further promote the adoption of alternative hosts for commercial protein expression.
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