Expanding the CRISPR/Cas9 Toolbox for Gene Engineering in S. cerevisiae

The yeast S. cerevisiae serves as a model organism for many decades. Numerous molecular tools have been developed throughout the years to engineer its genome. Specifically, homologous recombination protocols allowed gene deletion, replacement and tagging of almost every S. cerevisiae gene, thus enabling mechanistic understanding of various cellular processes. Recently, CRISPR/Cas9-based approaches have been adapted to the yeast system, simplifying the protocols to manipulate this organism. In CRISPR/Cas9 systems, guide-RNA directs a site-specific double-strand DNA cleavage by the Cas9 nuclease. The directed cleavage enhances homologous recombination events, thereby facilitating changes to desired genomic loci. The use of a single vector to express both guide-RNA and Cas9 enzyme may simplify genomic manipulations and was used to introduce double-strand breaks at artificial sites (Anand et al. in Nature 544(7650):377-380, 2017. https://doi.org/10.1038/nature22046) or within selection markers (Ryan et al. in Cold Spring Harbor Protoc, 2014. https://doi.org/10.1101/pdb.prot086827). Here, we generalize this approach to demonstrate its utility in modifying natural genomic loci. We devise vectors to perform common genetic manipulations in S. cerevisiae, including gene deletion, single-base mutations, introduction of site-specific polymorphism and tag insertion. Notably, a vector that efficiently cleaves within GFP was generated, allowing replacing a GFP tag with other sequences. This vector may be of utility for replacing any gene tagged with GFP by a sequence of choice. Importantly, we demonstrate the efficiency of chemically synthesized 80-mer homologous DNA as a substrate for recombination, alleviating the need for PCR steps in the procedure. In all presented applications, high efficiency of the expected gene alteration and no other change in the genomic loci were obtained. Overall, this work expands the repertoire of single-plasmid CRISPR/cas9 approaches and provides a facile alternative to manipulate the yeast genome.