title: Combinatorial optimization of CRISPR/Cas9 expression enables precision genome engineering in the methylotrophic yeast Pichia pastoris.
abstract: The methylotrophic yeast Pichia pastoris (Komagataella phaffii) is one of the most commonly used expression systems for heterologous protein production. However the recombination machinery in P. pastoris is less effective in contrast to Saccharomyces cerevisiae, where efficient homologous recombination naturally facilitates genetic modifications. The lack of simple and efficient methods for gene disruption and specifically integrating cassettes has remained a bottleneck for strain engineering in P. pastoris. Therefore tools and methods for targeted genome modifications are of great interest. Here we report the establishment of CRISPR/Cas9 technologies for P. pastoris and demonstrate targeting efficiencies approaching 100%. However there appeared to be a narrow window of optimal conditions required for efficient CRISPR/Cas9 function for this host. We systematically tested combinations of various codon optimized DNA sequences of CAS9, different gRNA sequences, RNA Polymerase III and RNA Polymerase II promoters in combination with ribozymes for the expression of the gRNAs and RNA Polymerase II promoters for the expression of CAS9. Only 6 out of 95 constructs were functional for efficient genome editing. We used this optimized CRISPR/Cas9 system for gene disruption studies, to introduce multiplexed gene deletions and to test the targeted integration of homologous DNA cassettes. This system allows rapid, marker-less genome engineering in P. pastoris enabling unprecedented strain and metabolic engineering applications.
authors.affiliation: Institute for Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria.
authors.forename: Astrid
authors.initials: A
authors.lastname: Weninger
authors.affiliation: Institute for Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria.
authors.forename: Anna-Maria
authors.initials: AM
authors.lastname: Hatzl
authors.affiliation: Institute for Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria.
authors.forename: Christian
authors.initials: C
authors.lastname: Schmid
authors.affiliation: Institute for Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria. Electronic address: thomas.vogl@aon.at.
authors.forename: Thomas
authors.initials: T
authors.lastname: Vogl
authors.affiliation: Institute for Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria.
authors.forename: Anton
authors.initials: A
authors.lastname: Glieder
mesh_terms: D064113:CRISPR-Cas Systems; D005818:Genetic Engineering; D010843:Pichia; D058615:Synthetic Biology
keywords: CRISPR/Cas9; Gene replacement by homologous recombination; Genome engineering; Multiplexing; Pichia pastoris; Synthetic biology