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A teaching protocol demonstrating the use of EasyClone and CRISPR/Cas9 for metabolic engineering of Saccharomyces cerevisiae and Yarrowia lipolytica.
Milne N, Tramontin LRR, Borodina I
FEMS Yeast Res. 2019 Sep 26. pii: foz062. doi: 10.1093/femsyr/foz062.
PubMed Article

We present a teaching protocol suitable for demonstrating the use of EasyClone and CRISPR/Cas9 for metabolic engineering of industrially relevant yeasts Saccharomyces cerevisiae and Yarrowia lipolytica, using β-carotene production as a case study. The protocol details all steps required to generate DNA parts, transform and genotype yeast, and perform a phenotypic screen to determine β-carotene production. The protocol is intended to be used as an instruction manual for a two-week practical course aimed at MSc and PhD students. The protocol details all necessary steps for students to engineer yeast to produce β-carotene and serves as a practical introduction to the principles of metabolic engineering including the concepts of boosting native precursor supply and alleviating rate-limiting steps. It also highlights key differences in the metabolism and heterologous production capacity of two industrially relevant yeast species. The protocol is divided into daily experiments covering a two week period and provides detailed instructions for every step meaning this protocol can be used 'as is' for a teaching course or as a case study for how yeast can be engineered to produce value-added molecules. All of the plasmids listed on this page are required to carry out the entire protocol.

Borodina EasyClone Figure

Notes:

  • The protocol can be found in the article listed above.
  • The yeast strains have been deposited at Euroscarf.
  • If you are interested in ordering all 33 plasmids, please contact [email protected] to ask about special pricing.

Plasmids from the Teaching Protocol

ID Plasmid Description   
73273 pCfB3035 (Empty Backbone) EasyClone-MarkerFree backbone vector for the addition of 1 or 2 genes and promoters for integration into site X-4 (Chr X: 236336..237310) Add to Cart
73276 pCfB2904 (Empty Backbone) EasyClone-MarkerFree backbone vector for the addition of 1 or 2 genes and promoters for integration into site XI-3 (Chr XI: 93378..94567) Add to Cart
73281 pCfB2909 (Empty Backbone) EasyClone-MarkerFree backbone vector for the addition of 1 or 2 genes and promoters for integration into site XII-5 (Chr XII: 839226..840357) Add to Cart
73294 pCfB3052 EasyClone-MarkerFree guiding RNA vector to direct Cas9 to cut at sites X-4, XI-3, and XII-5 Add to Cart
78230 p1977 Example plasmid containing a bidirectional promoter of pTDH3 and pTEF1 Add to Cart
78231 pCfB2312 Expresses Cas9 protein, under the control of the TEF1 promoter, and CYC terminator. KanMX resistance Add to Cart
78232 pTAJAK-71 (Empty Backbone) Empty vector, for the insertion of gRNA expression cassettes into the vector. Add to Cart
106151 pCfB6364 EasyCloneYALI system-based yeast integrative vector expressing Cas9 carrying D-serine marker, integration into Yarrowia lipolytica ku70 locus, amp resistance Add to Cart
106152 pCfB6682 (Empty Backbone) EasyCloneYALI system-based yeast integrative vector for markerfree integration via CRISPR/Cas9 to be used in combination with pCfB6627, integration into Yarrowia lipolytica chromosomal location IntC_2, USER site for cloning, amp resistance Add to Cart
106154 pCfB6684 (Empty Backbone) EasyCloneYALI system-based yeast integrative vector for markerfree integration via CRISPR/Cas9 to be used in combination with pCfB6631, integration into Yarrowia lipolytica chromosomal location IntD_1, USER site for cloning, amp resistance Add to Cart
106155 pCfB6677 (Empty Backbone) EasyCloneYALI system-based yeast integrative vector for markerfree integration via CRISPR/Cas9 to be used in combination with pCfB6632, integration into Yarrowia lipolytica chromosomal location IntE_1, USER site for cloning, amp resistance Add to Cart
106159 pCfB6627 EasyCloneYALI system-based yeast gRNA expression vector carrying a nourseothricin-resistance marker, helps to integrate vector pCfB6682 into Yarrowia lipolytica chromosomal location IntC_2, amp resistance Add to Cart
106161 pCfB6631 EasyCloneYALI system-based yeast gRNA expression vector carrying a nourseothricin-resistance marker, helps to integrate vector pCfB6684 into Yarrowia lipolytica chromosomal location IntD_1, amp resistance Add to Cart
106162 pCfB6633 EasyCloneYALI system-based yeast gRNA expression vector carrying a nourseothricin-resistance marker, helps to integrate vector pCfB6677 into Yarrowia lipolytica chromosomal location IntE_1, amp resistance Add to Cart
106166 pCfB3405 (Empty Backbone) EasyCloneYALI system-based yeast episomal vector carrying a nourseothricin-resistance marker for Yarrowia lipolytica, can be used for gRNA expression, amp resistance Add to Cart
126905 pCfB8739 Template for PCR amplification of XdCrtYB Add to Cart
126906 pCfB8740 Template for PCR amplification of XdCrtI Add to Cart
126907 pCfB8741 Template for PCR amplification of XdCrtE Add to Cart
126908 pCfB8742 Template for PCR amplification of pGPD1-pFBA1 double promoter biobrick for Yarrowia lipolytica Add to Cart
126909 pCfB8818 Template for PCR amplification of HMG1from Yarrowia lipolytica Add to Cart
126910 pCfB8792 Template for PCR amplification of ADE2 gRNA biobrick for targeting Saccharomyces cerevisiae ADE2 gene Add to Cart
126911 pCfB5191 Plasmid containing gRNA expression cassettes targeting the X-4 and XII-5 integration sites in Saccharomyces cerevisiae Add to Cart
126912 pCfB8622 Plasmid containing gRNA expression cassette targeting ADE2 in Saccharomyces cerevisiae Add to Cart
126913 pCfB8379 Plasmid containing integration cassette at X-4 integration site in Saccharomyces cerevisiae for overexpression of XdCrtI and XdCrtYB Add to Cart
126914 pCfB8380 Plasmid containing integration cassette at XII-5 integration site in Saccharomyces cerevisiae for overexpression of XdCrtE Add to Cart
126915 pCfB8381 Plasmid containing integration cassette at XI-3 integration site in Saccharomyces cerevisiae for overexpression of XdCrtI and tHMG1 Add to Cart
126916 pCfB8382 Plasmid containing integration cassette at XI-3 integration site in Saccharomyces cerevisiae for overexpression of XdCrtI Add to Cart
126917 pCfB8383 Plasmid containing integration cassette at XI-3 integration site in Saccharomyces cerevisiae for overexpression of tHMG1 Add to Cart
126918 pCfB8748 Plasmid containing integration cassette at IntE1 integration site in Yarrowia lipolytica for overexpression of XdCrtE Add to Cart
126919 pCfB8644 Plasmid containing integration cassette at IntC2 integration site in Yarrowia lipolytica for overexpression of XdCrtI and XdCrtYB Add to Cart
126920 pCfB8786 Plasmid containing integration cassette at IntD1 integration site in Yarrowia lipolytica for overexpression of XdCrtI Add to Cart
126921 pCfB8787 Plasmid containing integration cassette at IntD1 integration site in Yarrowia lipolytica for overexpression of HMG1 Add to Cart
126922 pCfB8788 Plasmid containing integration cassette at IntD1 integration site in Yarrowia lipolytica for overexpression of XdCrtI and HMG1 Add to Cart
Note: the plasmids listed below were deposited with the article, but they are more fully described in the complete table above.

Plasmids from Article

ID Plasmid Purpose
126905pCfB8739Template for PCR amplification of XdCrtYB
126906pCfB8740Template for PCR amplification of XdCrtI
126907pCfB8741Template for PCR amplification of XdCrtE
126908pCfB8742Template for PCR amplification of pGPD1-pFBA1 double promoter biobrick for Yarrowia lipolytica
126909pCfB8818Template for PCR amplification of HMG1from Yarrowia lipolytica
126910pCfB8792Template for PCR amplification of ADE2 gRNA biobrick for targeting Saccharomyces cerevisiae ADE2 gene
126911pCfB5191Plasmid containing gRNA expression cassettes targeting the X-4 and XII-5 integration sites in Saccharomyces cerevisiae
126912pCfB8622Plasmid containing gRNA expression cassette targeting ADE2 in Saccharomyces cerevisiae
126913pCfB8379Plasmid containing integration cassette at X-4 integration site in Saccharomyces cerevisiae for overexpression of XdCrtI and XdCrtYB
126914pCfB8380Plasmid containing integration cassette at XII-5 integration site in Saccharomyces cerevisiae for overexpression of XdCrtE
126915pCfB8381Plasmid containing integration cassette at XI-3 integration site in Saccharomyces cerevisiae for overexpression of XdCrtI and tHMG1
126916pCfB8382Plasmid containing integration cassette at XI-3 integration site in Saccharomyces cerevisiae for overexpression of XdCrtI
126917pCfB8383Plasmid containing integration cassette at XI-3 integration site in Saccharomyces cerevisiae for overexpression of tHMG1
126918pCfB8748Plasmid containing integration cassette at IntE1 integration site in Yarrowia lipolytica for overexpression of XdCrtE
126919pCfB8644Plasmid containing integration cassette at IntC2 integration site in Yarrowia lipolytica for overexpression of XdCrtI and XdCrtYB
126920pCfB8786Plasmid containing integration cassette at IntD1 integration site in Yarrowia lipolytica for overexpression of XdCrtI
126921pCfB8787Plasmid containing integration cassette at IntD1 integration site in Yarrowia lipolytica for overexpression of HMG1
126922pCfB8788Plasmid containing integration cassette at IntD1 integration site in Yarrowia lipolytica for overexpression of XdCrtI and HMG1

Antibodies from Article