We all know that yeast is a powerful eukaryotic model organism – its genome is easy to manipulate, it’s affordable, and it grows fast to boot. The yeast strains S. cerevisiae and S. pombe have dominated the research scene. But what about the other yeasts – in the biomedical world, are there even other yeasts? In this blog we will review an alternative model yeast strain and discuss why you may want to consider a yeast off the beaten path.
Yeast as a model organism
Yeast are single cell, eukaryotic organisms formally classified as fungi. They reproduce by either fission or budding, which is the primary distinction between two of the most frequently used yeast strains: S. pombe (fission) and S. cerevisiae (budding). Yeast make for an excellent model organism for a few reasons:
- Affordable to culture and easy to work with
- Grows extremely fast (doubling time of ~ 2 hours)
- Amenable to genetic manipulation
- The first eukaryote (S. cerevisiae) to have its genome fully sequenced
There are several human disease models established in yeast, including a widely used Parkinson’s experimental model. In fact, approximately 25% of yeast genes have a human counterpart, enabling study of human-relevant pathways (Liu et al., 2017). Beyond human relevance, yeast have many applications in food science and biotech due to its fermentation abilities and other useful traits.
The “biotech yeast”
You’re probably wondering if the “biotech yeast” is S. pombe or S. cerevisiae. Actually, it’s neither. The most commonly used yeast by biotech and pharmaceutical companies is K. phaffii (formerly known as pichia). What is this new-fangled yeast? It’s actually not new at all, but it’s not as well-known in the general research community.
Phillips Petroleum Company first commercially developed K. phaffii in the 1970s with the goal of producing high protein animal feed. Due to increasing prices of methanol and advancements in other biomass production techniques in the following decades, Phillips made the decision to release the K. phaffii expression system to the general research community in the 1990s when they abandoned the system. Since then, multiple biotech and pharmaceutical companies (along with some research laboratories) have picked up the system for some of the uses outlined below.
Biology
They say comparison is the thief of joy, but I think it’s acceptable if it’s in the name of beer and bread. The following table lists some of the biological commonalities and differences between K. phaffii and other yeast strains.
|
|
S. cerevisiae |
S. pombe |
K. phaffii |
|
Growth properties |
Facultative anaerobe |
Facultative anaerobe |
Obligate aerobe |
|
Number of chromosomes |
16 |
3 |
4 |
|
Preferred carbon source |
Glucose |
Glucose |
Glucose, methanol, glycerol |
|
Heterothallic mating |
Efficient |
Efficient |
Inefficient |
|
Ploidy |
Usually diploid, but spontaneously changes |
Usually haploid |
Usually haploid |
|
Pathology |
Non-pathogenic |
||
In short, K. phaffii is a non-pathogenic yeast that operates as an obligate aerobe. It’s also a methylotropic yeast, meaning it can utilize methanol as its sole source of carbon and energy (as well as glucose or glycerol). K. phaffii is only distantly related to S. pombe and S. cerevisiae; evolutionarily it evolved much slower and bears more similarity to the ancient yeast strains and metazoan cells.
Applications for K. phaffii
There’s a number of different uses for the phaffii-lous strain.
Protein expression
K. phaffii first gained attention for its powerful promoter of a gene important for methanol usage. This gene promoter, AOX1, was co-opted for the expression of recombinant proteins by the pharmaceutical and biotech industries as a protein expression workhorse. This yeast can also give more protein bang for your media buck - it grows at higher cell densities than most of its counterparts, yielding higher production power from a given flask volume. What’s even better? K. phaffii is highly efficient at protein secretion, making harvesting recombinant proteins a cinch. This is because it doesn’t secrete its own endogenous proteins, making the recombinant protein its major secretion.
Beyond sheer protein production, K. phaffii is exceptionally good for post-translational modification of recombinant protein products, specifically glycosylation. The native glycosylation machinery of K. phaffii lacks certain terminal mannose glycopeptides (which most other yeast possess) that are problematic for human administration. Thus, the production of glycoproteins for human therapies, such as antibodies, is possible in K. phaffii since it produces ‘human-like’ glycosylated proteins.
Peroxisome studies
Peroxisomes are small, membrane-bound organelles essential for sequestering certain enzymes and performing specific oxidative reactions. They are found in all eukaryotic cells and peroxisomes are where methanol metabolism occurs in methylotrophic organisms. K. phaffii is an excellent model for peroxisome studies since their peroxisomes will proliferate upon a media change into methanol and peroxisomal autophagy can be induced by removing methanol from the media. This feature makes the strain tractable for peroxisomal studies on biogenesis, degradation, and proliferation.
Genome manipulation
K. phaffii’s genome has been sequenced for some time, clearing the greatest hurdle for genome engineering. A unique evolutionary feature of K. phaffii, relative to S. cerevisiae, is that it predominantly uses non-homologous end joining (NHEJ) to perform DNA double strand break repair instead of homologous recombination (HR). HR is the preferred pathway for generating knock-in mutations, and NHEJ is an error-prone pathway frequently introducing frameshift knockout mutations. Thus, if genetic manipulation one way or the other (knock-in or knock-out) is essential to your work, you might want to pick a yeast strain best suited to it.
Putting K. phaffii to work
The yeast giants - S. cerevisiae and S. pombe - aren’t going anywhere anytime soon, and for good reason! However, there are other players in the game (even beyond K. phaffii ) worth looking into whether you’re just dipping your toes into the yeast world or have risen into yeast expertise!
References and Resources
References
Liu, Wei, et al., From Saccharomyces cerevisiae to human: The important gene co‑expression modules. Biomedical Reports 7.2 (2017): 153-158. DOI: 10.3892/br.2017.941
Bernauer L., et al., Komagataella phaffi as Emerging Model Organisms in Fundamental Research. Front. Microbiol. 11-2020, 2021. DOI: 10.3389/fmicb.2020.607028
Riley, R., et al., Comparative genomics of biotechnologically important yeasts. Proc. Natl. Acad. Sci., 113, 9882-9887. DOI: 10.1073/pnas.1603941113
Additional Resources on the Addgene Blog
- Five Popular Model Organisms
- Plasmids 101: Yeast Vectors
- Tips for Screening with the Yeast Two Hybrid System
Additional Resources on Addgene.org
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