Komagataella phaffii as Emerging Model Organism in Fundamental Research

Abstract

Komagataella phaffii (Pichia pastoris) is one of the most extensively applied yeast species in pharmaceutical and biotechnological industries, and, therefore, also called the biotech yeast. However, thanks to more advanced strain engineering techniques, it recently started to gain attention as model organism in fundamental research. So far, the most studied model yeast is its distant cousin, Saccharomyces cerevisiae. While these data are of great importance, they limit our knowledge to one organism only. Since the divergence of the two species 250 million years ago, K. phaffii appears to have evolved less rapidly than S. cerevisiae, which is why it remains more characteristic of the common ancient yeast ancestors and shares more features with metazoan cells. This makes K. phaffii a valuable model organism for research on eukaryotic molecular cell biology, a potential we are only beginning to fully exploit. As methylotrophic yeast, K. phaffii has the intriguing property of being able to efficiently assimilate methanol as a sole source of carbon and energy. Therefore, major efforts have been made using K. phaffii as model organism to study methanol assimilation, peroxisome biogenesis and pexophagy. Other research topics covered in this review range from yeast genetics including mating and sporulation behavior to other cellular processes such as protein secretion, lipid biosynthesis and cell wall biogenesis. In this review article, we compare data obtained from K. phaffii with S. cerevisiae and other yeasts whenever relevant, elucidate major differences, and, most importantly, highlight the big potential of using K. phaffii in fundamental research.

Histidine is essential for growth of Komagataella phaffii cultured in YPA medium

“…HIS4 is essential for optimal growth of K. phaffii cultured in YPA K. phaffii has emerged as an important host for the expression of several heterologous proteins and a model organism for fundamental research [14,15]. K. phaffii expression vectors generally contain auxotroph markers (e.g., HIS4, MET2, ADE1, ARG4) or antibiotic selectable markers (e.g., Zeocin, geneticin (G418) and blasticidin S).…”

Applying the auxin-based degron system for the inducible, reversible and complete protein degradation in Komagataella phaffii

“…In S. cerevisiae , ∼19% of the genes were found to be essential, based on the fact that spores carrying a deletion allele of these genes failed to germinate and form colonies under standard laboratory conditions – a method known as tetrad analysis ( Giaever et al., 2002 ). In contrast, there is very little knowledge about whether or not a gene is essential in K. phaffii , because tetrad analysis is extremely hard to implement as mating and sporulation are less effective and stable in this yeast (reviewed by ( Bernauer et al., 2021 )). A promising study analyzed the efficiency of random transposon insertion into the K. phaffii genome and, thereby made predictions about whether a gene is essential or not ( Zhu et al., 2018 ).…”

“…Pichia pastoris ) is a methylotrophic budding yeast that is known best for its extensive use as efficient protein production and secretion host in industrial applications. Lately, it started to gain attention as attractive alternative model yeast in fundamental research ( Bernauer et al., 2021 ). Although the genetic engineering of this yeast was substantially facilitated by novel tools such as CRISPR/Cas9 ( Weninger et al., 2018 ) and the construction of stable heterothallic strains ( Heistinger et al., 2017 ), its use in fundamental research is still underrepresented owing to a critical lack of advanced technologies.…”

A New Expression System Based on Psychrotolerant Debaryomyces macquariensis Yeast and Its Application to the Production of Cold-Active β-d-Galactosidase from Paracoccus sp. 32d

“…Methylotrophic yeast K. phaffii is currently considered to be one of the most effective and versatile platforms for the production of recombinant proteins, including biopharmaceuticals and industrial enzymes [ 6 , 26 ]. Moreover, it has recently started to gain attention as a model organism in fundamental research [ 27 ]. Most of the yeast expression hosts mentioned are mesophiles, with the exception of O. polymorpha and B. adeninivorans , which are thermotolerants [ 21 , 25 ].…”