An Introduction to Yeast

Yeast are a fascinating group of diverse microorganisms that have played a pivotal role in human history. For thousands of years, yeast have been used to make bread, beer, wine, and other fermented foods and beverages. Yeast are one of our first biotechnology tools, and are intrinsically linked to the rise of human civlization!

Yeast have also been instrumental in our understanding of biology. In the 19th century, Louis Pasteur established the link between yeast and fermentation. Then, in the early 20th century, Eduard Buchner demonstrated through yeast cell-free extracts that the enzymes within yeast cells were responsible for fermentation. By the 20th century, genetic manipulation of yeast became possible, opening up new applications for yeast in biotechnology.

As eukaryotic microorganisms with well-characterized genomes, yeast are useful model organisms that have greatly aided our understanding of genetics, molecular biology, and metabolic engineering.

Saccharomyces cerevisiae, SEM image. Attribution to Mogana Das Murtey and Patchamuthu Ramasamy. https://www.intechopen.com/chapters/49652

This, in turn, has led yeast to become powerful tools as synthetic biology chassis. Within iGEM, yeast are the second most common chassis group used in projects, just behind E. coli.

On this page, we will discuss yeast's role in synthetic biology and iGEM, along with some helpful resources. As mentioned, yeast are a diverse group of microorganisms, but here on, when we refer to "yeast," we will be considering only a few well-characterized species that are commonly used in synthetic biology.

Why are Yeast chassis useful?

There are several benefits to using yeast as a chassis in synthetic biology:

  • Well-characterized genetics: A yeast species like Saccharomyces cerevisiae has a well-characterized genome and has been used as a model organism for decades, allowing for a deeper understanding of the yeast's cellular processes and mechanisms. Many of the genetic tools and techniques developed for a yeast species are well-established,
  • Eukaryotic cell structure: Yeast are eukaryotic microorganisms, meaning that they have a nucleus and other membrane-bound organelles. This makes them more similar to human cells than prokaryotes like bacteria, and allows for more accurate modeling of complex cellular processes.
  • More complex post-translational modifications: Yeast are capable of performing a wider range of (and more complex) post-translational modifications. These modifications are important for the functionality of many proteins, including therapeutic proteins, and yeast can produce these proteins with a higher degree of accuracy than bacteria.
  • Ease of genetic manipulation: Yeast are relatively easy to grow and genetically manipulate. This allows for the creation of engineered yeast strains that can produce valuable compounds such as biofuels and pharmaceuticals.
  • Scalability: Yeast are relatively fast-growing microorganisms that can be grown in large quantities in industrial bioreactors. This makes them an attractive platform for large-scale production of valuable compounds.

Commonly Used Chassis

The three yeast species below are widely used as host chassis in synthetic biology due to their versatility, ease of genetic manipulation, and ability to produce high levels of valuable compounds. The choice of chassis will depend on the specific application and the desired product, as each chassis has its own unique advantages and limitations.

Saccharomyces cerevisiae

S. cerevisiae, also known as baker's yeast or brewer's yeast, is one of the most extensively studied and widely used yeast strains in biotechnology. It is a versatile organism that can ferment a wide range of sugars and produce a variety of useful products, including ethanol, organic acids, and amino acids. S. cerevisiae is also commonly used as a host organism for the production of heterologous proteins, such as therapeutic proteins or industrial enzymes.

Komagataella phaffii (Pichia pastoris)

Like S. cerevisiae, Pichia is a versatile yeast species used in industrial biotechnology. It can grow on a wide range of carbon sources and produce high levels of heterologous proteins. However, P. pastoris has several advantages over S. cerevisiae, including its ability to perform more complex post-translational modifications and its tolerance for higher expression levels of heterologous proteins. P. pastoris is commonly used for the production of therapeutic proteins, industrial enzymes, and vaccines.

Yarrowia lipolytica

Yarrowia lipolytica is a yeast strain that grows on a variety of carbon sources, including hydrophobic substrates such as lipids and fatty acids. This makes it an attractive platform for the production of biofuels and other high-value compounds derived from lipid metabolism. Y. lipolytica is also commonly used for the production of heterologous proteins, such as enzymes and bioactive peptides.

Yeast in iGEM

iGEM Teams have been working in yeast for almost two decades (almost as long as iGEM has existed)! As the second most commonly used chassis in iGEM, there are over a hundred projects, and even more parts, to learn from and build upon. We will be building a database of yeast projects, but here are just a few team projects that may be of interest.

  • The 2018 Groningen Team wanted to extricate the production of styrene from our current petrochemical-based economy, an unsustainable and environmentally unfriendly process. They aimed to create their StyGreen bioplastic from cellulose waste, all in Saccharomyces cerevisiae. By breaking their overall design down, they were able to demonstrate their purified enzymes ability to degrade cellulose, their S. cerevisiae strain's ability to grow on cellulose, and its production of styrene from glucose.
  • The 2019 Evry Paris-Saclay Team sought to produce medically important Conjugated Linolenic Acids (CLnAs) using Yarrowia lipolytica. Using it's lipid biosynthesis to their advantage, they hoped to sustainably produce two CLnAs, jacaric acid and punicic acid, in Yarrowia lipolytica's that are normally produced in Blue Jacaranda and pomegranate trees. They demonstrated a proof-of-concept by producing small amounts of punicic acid, developed a Loop compatible parts and plasmid collection, and measured GFP and RFP using calibrants, all in Y. lipolytica.
  • The 2022 DKU Team ↗ wanted to develop a non-antibiotic treatment to Shigella infections by engineering a probiotic yeast. Using Saccharomyces cerevisiae as their chassis, they wanted to develop a cell surface display system with Single VH domain (VHH) antibodies that would reduce the virulency of _Shigella through antibody-pathogen binding. They were able to design an antibody capable of binding IpaD, a Shigella-exclusive antigen, and demonstrate the antibody on the cell surface of their yeast strain.

Open Yeast Collection

Yeast toolkits provide a standardized set of genetic parts with known functions that can be combined to create new genetic constructs or pathways. A toolkit can simplify the process of assembly and enable rapid prototypying and testing of genetic constructs. It can also facilitate the sharing of information, as they provide a common language and framework.

There a few different yeast toolkits, but within iGEM, we have the Open Yeast Collection (OYC) within the iGEM Distribution. The OYC is a versatile open DNA toolkit for engineering Saccharomyces cerevisiae and Komagataella phaffii (Pichia pastoris), with a recently developed expansion for Yarrowia lipolytica. The collection enables anyone to have a robust toolkit to build new metabolic pathways or produce enzymes and proteins of interest in yeast through Golden Gate Assembly. The OYC is a great starting point for your yeast synthetic biology projects. For a more indepth look see the Open Yeast Collection page below.

The Open Yeast Collection was developed by Scott Pownall, PhD ↗ in collaboration with Open Bioeconomy ↗ and FreeGenes ↗.

Open Yeast Collection part types

Safety Check-in

For iGEM teams planning to use yeast in their projects, please make sure to review iGEM's safety policies. While a yeast species like S. cerevisiae is considered a RG1 organism, due to its spore-forming nature, it is not on the iGEM white list and will require a safety check-in. For more information, please see this blog post!

Additional Yeast Resources

The content of this page was developed with Scott Pownall, PhD ↗ (creator of the the Open Yeast Collection ↗!) and the Open Science Network Society ↗.

Overview

announcement

Open Yeast Collection: Updates coming soon!

We will have more information on the Open Yeast Collection coming soon! This will include well locations for the collection in the 2024 Distribution, the new expansion with parts for the Yeast Protein Expression Toolkit, and more!!

The Open Yeast Collection (OYC) is a versatile open DNA toolkit for engineering Saccharomyces cerevisiae and Komagataella phaffii (Pichia pastoris), with a recently developed expansion for the Yeast Protein Expression Toolkit.

The collection permits the building of modular plasmids using Golden Gate Assembly from free, reusable and redistributable genetic parts. Certain parts permit directly modifying yeast chromosomes through genome integration using homologous recombination and others permit episomal maintenance of plasmids carrying payloads.

The Open Yeast Collection (OYC) was first developed by Scott Pownall, PhD ↗ in collaboration with Open Bioeconomy ↗ and FreeGenes ↗.

Representation of the Open Yeast Collection configuration for assembling Integration Vectors

What are the parts?

The Open Yeast Collection contains the following parts:

  • Yeast promoters - strong, medium, weak and inducible
  • Secretion tags and nuclear localization signal
  • CDS - genes for metabolic pathways
  • Yeast terminators
  • Yeast selection markers - for positive and negative selection options
  • Yeast homology regions - for integration into the yeast genome
  • Yeast origins - for episomal maintenance and transfer of plasmids
  • Left & right assembly connectors
  • E. coli selection markers and 2 origins of replication
  • Assembly bridges for optional bypassing of assembly positions.

Open Yeast Collection II Expansion

The 2024 Distribution includes an expansion to the Open Yeast Collection. This expansion includes parts permitting the integration with the SEVA plasmid system ↗, and the creation of an adaptation and extension of the E. coli Protein Expression Toolkit for use in yeast.

More on this to come!

Where are the parts (in the Distribution)?

The Open Yeast Collection is available in the following iGEM Distributions

Please note, that each release of the Open Yeast Collection as part of an iGEM Distribution may see changes to the available samples from the collection. This may be due to quality control, manufacturing issues, deprecation, or expansion. Be sure to view the platemap that matches your iGEM Distribution's release year, to view the collection's contents and well locations.

The OYC Assembly Syntax

The OYC uses the same MoClo and iGEM Type IIS fusion sites for assembling the transcription unit: promoter, 5’ untranslated region (RBS in prokaryotes), cds, and terminator. This ensures maximum compatibility to a variety of other toolkits and destination vectors.

However, the OYC has additional fusion sites that extend the functionality of the collection. Below is an example of the parts one could select to assemble an integrative Pichia pastoris expression construct. The BsaI overhangs of each part are listed as prefix (5’ fusion site) and suffix (3’ fusion site).

Example of the parts one could select to assemble an integrative Pichia pastoris expression construct

2022 Webinar

As part of its 2022 webinar series, the iGEM Engineering Committee hosted Working with the Open Yeast Collection, an Introduction with Scott Pownall, PhD. This webinar serves as an introduction to the Open Yeast Collection, its contents, framework, and how one might utilize it.

Please note that the webinar references parts and their samples that were in the 2022 iGEM Distribution. For the collection's current contents (and well locations), please make sure you are viewing the platemap of your current iGEM Distribution.

Additional Resources

The content of this page was developed by Scott Pownall, PhD ↗ (creator of the the Open Yeast Collection ↗!) and the Open Science Network Society ↗.