CRISPR/Cas9-Mediated Homology-Directed Genome Editing in Pichia pastoris

  • Thomas Gassler
  • Lina Heistinger
  • Diethard Mattanovich
  • Brigitte Gasser
  • Roland PrielhoferEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1923)


State-of-the-art strain engineering techniques for the methylotrophic yeast Pichia pastoris (syn. Komagataella spp.) include overexpression of endogenous and heterologous genes and deletion of host genes. For efficient gene deletion, methods such as the split-marker technique have been established. However, synthetic biology trends move toward building up large and complex reaction networks, which often require endogenous gene knockouts and simultaneous overexpression of individual genes or whole pathways. Realization of such engineering tasks by conventional approaches employing subsequent steps of transformations and marker recycling is very time- and labor-consuming. Other applications require tagging of certain genes/proteins or promoter exchange approaches, which are hard to design and construct with conventional methods. Therefore, efficient systems are required that allow precise manipulations of the P. pastoris genome, including simultaneous overexpression of multiple genes. To meet this challenge, we have developed a CRISPR/Cas9-based kit for gene insertions, deletions, and replacements, which paves the way for precise genomic modifications in P. pastoris. In this chapter, the versatile method for performing these modifications without the integration of a selection marker is described. A ready-to-use plasmid kit for performing CRISPR/Cas9-mediated genome editing in P. pastoris based on the GoldenPiCS modular cloning vectors is available at Addgene as CRISPi kit (#1000000136).

Key words

Pichia pastoris Synthetic biology Genome editing GoldenPiCS CRISPR/Cas9 



This work was supported by the Federal Ministry for Digital and Economic Affairs (BMDW), the Federal Ministry of Traffic, Innovation and Technology (BMVIT), the Styrian Business Promotion Agency SFG, the Standortagentur Tirol, the Government of Lower Austria and ZIT-Technology Agency of the City of Vienna through the COMET-Funding Program managed by the Austrian Research Promotion Agency FFG; and the Austrian Federal Ministry for Digital and Economic Affairs (BMDW), the National Foundation for Research, Technology and Development and the Christian Doppler Research Association. TG and LH were supported by the Austrian Science Fund (FWF): Doctoral Program BioToP—Biomolecular Technology of Proteins (FWF W1224). We further want to thank Franz Zehetbauer and Dariusz Yarych for technical support as well as Corinna Rebnegger and Matthias Steiger for initial inspiration and fruitful discussions.


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Thomas Gassler
    • 1
    • 2
  • Lina Heistinger
    • 1
    • 3
  • Diethard Mattanovich
    • 5
  • Brigitte Gasser
    • 5
    • 4
  • Roland Prielhofer
    • 1
    • 2
    Email author
  1. 1.Department of BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
  2. 2.Austrian Centre of Industrial Biotechnology (acib)ViennaAustria
  3. 3.Christian Doppler Laboratory for Innovative Immunotherapeutics, Department of BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)ViennaAustria
  4. 4.Christian Doppler Laboratory for Growth-Decoupled Protein Production in Yeasts, Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU)ViennaAustria
  5. 5.Department of BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU) and Austrian Centre of Industrial Biotechnology (acib)ViennaAustria

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