mazF-mediated deletion system for large-scale genome engineering in Saccharomyces cerevisiae

A new mazF-based strategy for large-scale and scarless genome rearrangements in Saccharomyces cerevisiae was developed. We applied this method to delete designed internal (26.5 kbp) and terminal (28.9 kbp) regions located on the left arm of the chromosome XI of S. cerevisiae BY4741. The number of transformants was increased by one order of magnitude and about 90% of tested colonies were desired integrants using in vivo assembled deletion cassette containing longer flanking homology. Compared to conventional URA3 marker, in the counter-selection process, the new system generated 2–13 folds more colonies and the ratio of deletant was simultaneously elevated by 20–24%.