What’s wrong with SwYG? Reaching the limits of S. cerevisiae molecular and analytical toolbox

Ewout Knibbe, Eline D. Postma, Francine J. Boonekamp, Sofiia Dashko, Jordi Geelhoed, Anne-Marijn Maat, Marijke A.H. Luttik, Marcel van den Broek, Pascale Daran-Lapujade

The construction of powerful cell factories requires extensive remodelling of microbial genomes, entailing many rounds of transformations to perform the large number of desired gene modifications. However, increasing the number of genetic interventions inevitably increases the occurrence of unwanted mutations and effects. Using glycolysis as paradigm, a previous study developed a Saccharomyces cerevisiae strain in which the glycolytic genes, relocated to a single locus, can be easily swapped by any new design, thereby enabling fast and easy remodelling of the entire pathway. After 27 genetic modifications performed in 43 transformation rounds, the Switchable Yeast Glycolysis (SwYG) strain grew ca. 20% slower than its ancestor with the same glycolytic genes with native glycolysis design. Exploring the cause of this slower growth rate, the present study reflects on the genetic and analytical challenges encountered by extensive strain construction programs and provides design guidelines for integration of large constructs in the yeast genome. This study also suggests a potential involvement of the yeast glycolytic enzyme phosphoglycerate kinase (Pgk1) in PI(3)P synthesis and autophagy, as found in mammalian cells.

Includes supplemental figures and tables with descriptions of their content.