CRISPR/Cas9-Mediated Genome Editing of the Komagataella phaffii to Obtain a Phytase-Producer Markerless Strain

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Artur A. Tkachenko^1,a*, Larisa N. Borshchevskaya¹, Sergey P. Sineoky¹, and Tatiana L. Gordeeva¹

¹National Research Center “Kurchatov Institute”, 117545 Moscow, Russia

^* To whom correspondence should be addressed.

Received April 19, 2023; Revised April 19, 2023; Accepted May 19, 2023

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Using CRISPR/Cas9 system, the recipient strains K. phaffii VKPM Y-5013 (His^– phenotype) and K. phaffii VKPM Y-5014 (Leu^– phenotype) were derived from the K. phaffii VKPM Y-4287 strain, which has a high expression potential. Based on the developed recipient strains, markerless producers of heterologous proteins could be obtained. Efficiency of the gene inactivation with different variants of sgRNA ranged from 65 to 98% and from 15 to 72% for the HIS4 and LEU2 genes, respectively. The recipient strains retained growth characteristics of the parent strain and exhibited high expression potential, as estimated by the production of heterologous phytase from Citrobacter gillenii. Average productivity of the transformants based on the K. phaffii VKPM Y-5013 and K. phaffii VKPM Y-5014 strains was 2.1 and 2.0 times higher than productivity of the transformants of the commercial K. phaffii GS115 strain. Method for sequential integration of genetic material into genome of the K. phaffii VKPM Y-5013 strain was proposed. A highly effective multicopy markerless strain producing C. gillenii phytase was obtained.

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KEY WORDS: CRISPR/Cas9, Komagataella phaffii, genome editing, phytase, Citrobacter gillenii

DOI: 10.1134/S0006297923090134

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