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Quick and easy CRISPR engineering in Saccharomyces cerevisiae

Contributed by:
 WILLIAM SHAW, ELLIS LAB, Graduate student in the Ellis lab

Introduction

Saccharomyces cerevisiae has long been the most tractable organism for eukaryotic cell biology, owing to its genetic malleability, greatly facilitated by a preference for homologous recombination (HR) over non-homologous end joining (NHEJ) for double stranded break (DSB) repair. Over the years, biologists have taken advantage of this preference, allowing for the site-specific installation of genetic material and genomic edits with base-pair precision (Moqtaderi and Geisberg, 2013).

However, the demands on yeast engineering have significantly increased with the design of more complex systems and extensive metabolic pathways. Genetic techniques that have historically relied on marker recycling are proving too cumbersome to keep up with the ambitions of synthetic biologists.

How can CRISPR/Cas9 help edit the yeast genome?

Since the initial reports of CRISPR/Cas9 mediated genome editing in yeast by Dicarlo et al. in 2013, a diverse number of novel strategies have been developed for Cas9 and guide RNA expression, allowing highly efficient genome editing that can be multiplexed without the need for a marker (see Jakočiūnas et al., 2016 for a review on these).

Two of these new strategies are particularly powerful, improving the structure of the sgRNA – allowing for high expression and stability of the sgRNA in yeast (Ryan et al., 2014), as well as the method of sgRNA delivery – selecting for cells proficient in gap repair (Horwitz et al., 2015). Combined, these two advancements allow for high-efficiency, markerless editing of the yeast genome, aiding the work flow within the Ellis Lab.

How can CRISPR/Cas9 change the daily workflow of the yeast engineering?

CRISPR/Cas9 can be used for a number of strain engineering purposes, including:

  • Markerless integration of multiple genetic cassettes into selected genomic loci
  • Multiplexed and iterative gene knockouts without the need to recycle a marker
  • Precise genome editing – nucleotide substitutions, etc.

The greatest impact of CRISPR/Cas9 to the daily workflow of the yeast synthetic biologist is likely to be the integration of multiple expression cassettes into the genome without the need for a marker. Chromosomal integration has several benefits over vector based maintenance of foreign DNA:

  • Reliable and stable gene expression
  • Strain stability without the need for complex growth media
  • Lower heterogeneity within the yeast population

Fig 1 highlights the importance of genomic integration for stable, robust and repeatable expression. Although plasmid toolkits allow for the routine integration of genetic cassettes into the yeast genome, there is still a need to identify colonies that have integrated the exogenous DNA using a selectable marker. As markers are limited, even in laboratory auxotrophic strains, they can quickly become used up as a project becomes more complex, limiting strain development further down the line.

Fig 1. Comparing noise in plasmid and genomic expression of two fluorescent proteins. Proteins mRuby2 (false-coloured red) and Venus (false-coloured green) were expressed in the same cell with a strong, pTDH3 promoter. (A) Fluorescent proteins expressed on two separate CEN plasmids; (B) in tandem on a single CEN plasmid; (C) integrated into two different loci (LEU2 and URA3) in the S. cerevisiae genome; and (D) integrated in tandem at a single locus (URA3) in the genome. Each image was auto-exposed for both red and green channels, with yellow showing co-expression of mRuby2 and Venus. The variability in the relative expression of the two fluorescent proteins is reduced by moving from two plasmids to one, and the variability in total expression is reduced by moving to the genome. The difference between integrating into one or two loci in the genome is minimal. (Figure and legend taken from Ryan et al., 2014)

Conclusion

CRISPR/Cas9 avoids this complication as the integration of DNA into the yeast genome has become so efficient that selection is no longer a necessity, rather, a small handful of colonies can be screened using a simple colony PCR to validate successful integration. Furthermore, integration can be multiplexed, and is amenable to randomized library approaches (Horwitz et al., 2015), permitting a plethora of permutations to be assembled within a single transformation. For this reason, CRISPR/Cas9 and markerless integration of expression cassettes should be considered as a standard for introducing genes of interest into yeast, and a number of parts have been generated in the Ellis Lab to facilitate this (see parts list).


The engineered CRISPRm platform – Ryan et al., 2014

A recent advancement in yeast CRISPR/Cas9 technology was the development of highly persistent intracellular sgRNAs via the fusion of a 5’ HDV ribozyme and a yeast tRNA (Ryan et al., 2014). The addition of the tRNA allows the use of a host species specific promoter, which has been one of the limiting factors in achieving high levels of sgRNA expression in a number of organisms.

The ribozyme was included to serve serve two purposes:

  • To increase the stability of the sgRNA within the cells.
  • To catalyse the removal of the tRNA after transcription, via self-cleavage, to uncouple the sgRNA from the translation apparatus (Fig. 2).

Combined, these two structures improved the efficiency of gRNAs enough to make multiplexed CRISPR/Cas9 genome editing possible without the need for selection.

Fig. 2. The engineered CRISPRm platform. a) The mature sgRNA contains a 5′ hepatitis delta virus (HDV) ribozyme (δR), 20mer target sequence (guide), sgRNA and RNA polymerase III terminator. The RNA polymerase III promoter tRNA is catalytically removed by the HDV ribozyme (red arrow). B) Efficiency of multiplex insertion of DNA in diploid yeast cells with the 5′ HDV ribozyme (black) and without the 5′ HDV ribozyme (red). Triplex targeting without the 5′ HDV ribozyme was not tested. The tRNATyr promoter was used in these experiments. (Figure and legend taken from Ryan et al., 2014).

Selection of yeast cells proficient in gap repair – Horwitz et al., 2015

Another important development in yeast CRISPR/Cas9 was the novel delivery of sgRNA into yeast cells, by introducing the vector as linear DNA fragments that have to be assembled by the yeast HR machinery to reconstitute the sgRNA expression vector (Fig. 3). Horwitz et al. (2015) proposed that this ‘gap repair identifies a special subpopulation of transformed cells’:

‘Competency for homologous recombination is known to vary throughout the cell cycle, and the asynchronous mixture of log-phase cells used for transformation would be expected to contain cells in all states. If yeast cells most proficient in gap repair are also best equipped to accomplish multiplex integrations, then this capability may allow markerless, multiplex integrations to proceed with only transient expression of the sgRNAs.’

Although it must be noted that this method requires initial integration of Cas9 into the genome, under a medium/weak promoter.

Fig. 3. Gap repair of the sgRNA expression vector. The sgRNA expression vector is introduced into yeast cells constitutively expressing Cas9 in two linearized fragments with homology to each other. Once transformed into yeast, the HDR machinery will gap repair the plasmid, reconstituting the sgRNA expression vector. As a marker is also within the plasmid, only cells that have repaired the plasmid may survive in selective media. This selects for a subpopulation of cells that are most proficient in gap repair, increasing the likelihood that colonies will have integrated the donor DNA that was introduced alongside the linearized sgRNA vector components. Therefore, high efficiency gene editing can be achieved. (Figure adapted from Horwitz et al. (2015) and Walter et al. (2016)).

Ellis Lab sgRNA and Cas9 expression tools

How were the Ellis Lab CRISPR/Cas9 tools developed?

The Ellis Lab Cas9 and sgRNA expression tools were developed using the Yeast MoClo Toolkit (YTK), produced by Lee et al. (2015) at UC Berkeley, along with additional parts created by ourselves. These new tools combine the highly efficient sgRNA structure, yeast optimised Cas9 ORF, and the novel sgRNA delivery based on the gap repair of linearized fragments (Ryan et al., 2014; Horwitz et al., 2015). Furthermore, the Cas9 ORF was incorporated into the sgRNA expression vector so it may be introduced into the cell at the same time, removing the necessity of constitutive expression of Cas9 from the genome.

What does the toolkit have?

The toolkit consists of:

  • An sgRNA entry vector (Fig. 4a)
  • A range of Cas9-sgRNA expression vectors (Fig. 4b) with different selection markers
  • Markerless integration cassettes for the Ura3, Leu2 and HO loci, in the YTK format.
Fig 4. Ellis lab CRISPR/Cas9 tools. (a) the sgRNA entry vector (pWS082), is completed using small fragment Golden Gate assembly with two 26-mer oligos. Once assembled, the plasmid is then digested with EcoRV to create a linear sgRNA expression cassette. (b) The Cas9-sgRNA expression vector is linearized with a BsmBI restriction digest and gel purified. A range of gap repair vectors are available with different selection markers, each containing Cas9 under the expression of either the strong or medium strength promoter of Pgk1 and Rpl18B, respectively (see parts list).

How do you use the toolkit?

The sgRNA vector is completed using small fragment Golden Gate assembly (see protocols), which is digested with EcoRV to generate a linearized expression cassette. This linearized cassette has 500 bp arms with exact homology to the Cas9-sgRNA expression vector, and will gap repair the the linearized preparation of this plasmid in yeast to to reconstitute a stable Cas9-sgRNA expression vector (Fig. 5b). The marker on the Cas9-sgRNA vector can be used to select for successfully transformed cells expressing both Cas9 and an sgRNA.

Fig 5. Transformation and gap repair of linearized Cas9-sgRNA expression components for efficient markerless genome editing. (a) co-transformation of a digested sgRNA pool, linearized Cas9-sgRNA gap repair vector and donor DNA. (b) gap repair of the Cas9-sgRNA expression vector by the sgRNA expression cassette.

How do you use the toolkit to perform multiplexed Cas9 targeting?

As the sgRNA cassette and Cas9-sgRNA gap repair vector are always in the same format, once the sgRNA cassette has been linearized it can be used with any Cas9-sgRNA gap repair vector, and in combination with any other linearized sgRNA cassette, allowing for multiplexed Cas9 targeting (Fig. 5). Although only one linearized sgRNA cassette gap repairs the Cas9-sgRNA expression vector, it seems that expression from the linear pool of intracellular sgRNAs is sufficient, and editing is likely to occur early on within the first mother cell. We have successfully used up to 8 sgRNAs within a single transformation.

How do you perform iterative editing?

Although incredibly powerful, multiplexed CRISPR/Cas9 has its limitations. Selecting more than 3-4 targets to edit on the yeast genome will begin to stretch the capabilities of markerless editing beyond what is a reasonable number of transformants to screen. Despite advances we have made towards in silico prediction of gRNA ‘on-target scores’, in reality, efficiencies will be influenced by other factors, such as local chromatin structure. This makes it incredibly hard to forecast how successful any particular multiplexed edit will perform.

To address the limitations of CRISPR/Cas9 multiplexed editing, we explored other solutions to speed up cell line development requiring a large number of modifications. We identified 3 markers that can be used to iteratively perform edits without the need to cure the cells of the previous CRISPR/Cas9 machinery, by simply transforming the cells with plasmids containing the next marker in the cycle (Fig. 6).

Fig. 6. Marker cycling of the CRISPR/Cas9 machinery for iterative editing. 3 markers are sufficient to iteratively edit yeast without the interference of previous markers in the cycle. The markers URA3, LEU2, and HIS3 are used in the Ellis Lab, although any combination of markers should be possible.

A single rotation around the cycle is sufficient to arrive at zero background from the initial marker. i.e. If you start by using the URA3 marker, once you return to the URA3 marker, you will not get any growth from untransformed cells on a uracil deficient plate.

This makes it possible to immediately transform cells, once they have been validated by colony PCR, reducing the time between edits by several days. Using this workflow, and multiplexing 3-4 edits per transformation, it is possible to achieve 9-12 edits within 2 weeks.


Parts list

sgRNA entry vector

Name sgRNA promoter Yeast marker E.coli marker
pWS082 tRNAPhe N/A AmpR

Cas9-sgRNA gap repair vectors

Name Cas9 promoter Yeast marker E.coli marker
pWS158 pPGK1 Ura3 KanR
pWS171 pPGK1 Leu2 KanR
pWS172 pPGK1 His3 KanR
pWS173 pPGK1 KanR KanR
pWS174 pPGK1 NatR KanR
pWS175 pPGK1 HygR KanR
pWS176 pPGK1 ZeoR KanR
pWS160 pRPL18B Ura3 KanR
pWS177 pRPL18B Leu2 KanR
pWS178 pRPL18B His3 KanR
pWS179 pRPL18B KanR KanR
pWS180 pRPL18B NatR KanR
pWS181 pRPL18B HygR KanR
pWS182 pRPL18B ZeoR KanR

Markerless integration cassettes

Name Integration loci Yeast marker E.coli marker
pWS471 Ura3 N/A KanR
pWS472 Leu2 N/A KanR
pWS473 HO N/A KanR

sgRNAs for markerless integration

Name Integration loci Yeast marker E.coli marker
gWS044 Ura3 N/A AmpR
gWS042 Leu2 (1/2) N/A AmpR
gWS043 Leu2 (2/2) N/A AmpR
gWS045 HO N/A AmpR

Links to loci for integration (BY4741)


Protocols

sgRNA design, assembly and preparation

To design and analyse your guide RNAs please refer to Designing and Analysing Guide RNAs on the tutorial page of Benchling for an overview of how to choose your guide RNA in a particular region of the yeast genome. You can then refer to sgRNA Small Fragment Assembly for a protocol on assembling your two short oligos into the sgRNA entry vector (pWS082). Once assembled and sequence verified, the sgRNA expression cassette needs to be linearized with EcoRV. sgRNAs can be pooled with other sgRNAs and digested together. The entire mixture is then added to the remaining CRISPR components (linearized Cas9-sgRNA gap repair vector and donor DNA) and transformed directly into yeast. See sgRNA preparation for details on digestion conditions.

Cas9-sgRNA gap repair vector linearization

Before using any Cas9-sgRNA gap repair vector it should be linearized using BsmBI and gel purified. It is easiest to create a linearized stock of each vector by digesting and purifying an entire miniprep of the plasmid and setting the concentration to 100 ng/ml. Each transformation requires 100 ng of the gap repair vector, so should last a long time.

Markerless integration cassettes

Markerless cassettes have been created to be fully compatible with the YTK hierarchical workflow, and once complete, can be integrated with the aid of the CRISPR/Cas9 machinery (gRNAs for targeting the markerless integration cassettes also in the parts list. Before transforming, integration cassettes require digestion with NotI (see final part of Yeast Transformation – High efficiency for digestion conditions). For more information on how to use the YTK toolkit, see supplementary information in Lee et al.

Transformation guidelines

For transformation of CRISPR components, a high-efficiency transformation protocol should be used. The Yeast Transformation – High efficiency protocol is sufficient for routine CRISPR/Cas9 experiments, however, for multiplex experiments with 3 or more edits, it is recommended you use Yeast Transformation – Super-High efficiency.

For genome editing you will need 3 DNA components:

  • 100 ng of linearized Cas9-sgRNA gap repair vector
  • 200 ng of each digested sgRNA vector
  • > 2 µg of PCR amplified donor DNA OR 2 µg of each digested markerless integration cassette

These are rough guidelines that seem to work pretty well. The linearized Cas9-gRNA expression vector and sgRNA seem to work well at these amounts, however the amount of donor DNA will vary widely with your particular application and design – this will be down to your best judgment, however, larger amount of donor DNA seem to overcome efficiency problems. This can require anything up to 5 µg DNA of each donor.


References

  • DiCarlo, J. et al. Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Research 41, 4336-4343 (2013).
  • Horwitz, A. et al. Efficient Multiplexed Integration of Synergistic Alleles and Metabolic Pathways in Yeasts via CRISPR-Cas. Cell Systems 1, 88-96 (2015).
  • Jakočiūnas, T., Jensen, M. & Keasling, J. CRISPR/Cas9 advances engineering of microbial cell factories. Metabolic Engineering 34, 44-59 (2016).
  • Lee, M., DeLoache, W., Cervantes, B. & Dueber, J. A Highly Characterized Yeast Toolkit for Modular, Multipart Assembly. ACS Synth. Biol. 4, 975-986 (2015).
  • Moqtaderi, Z. & Geisberg J. Construction of Mutant Alleles in Saccharomyces cerevisiae without Cloning: Overview and the Delitto Perfetto Method. Curr Protoc Mol Biol. 104, 13.10C.1–13.10C.17 (2013).
  • Ryan, O. et al. Selection of chromosomal DNA libraries using a multiplex CRISPR system. eLife 3, (2014).

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