Engineering oxygen-independent biotin biosynthesis in Saccharomyces cerevisiae

An oxygen requirement for de novo biotin synthesis in Saccharomyces cerevisiae precludes the application of biotin-prototrophic strains in anaerobic processes that use biotin-free media. To overcome this issue, this study explores introduction of the oxygen-independent Escherichia coli biotin-biosynthesis pathway in S. cerevisiae. Implementation of this pathway required expression of seven E. coli genes involved in fatty-acid synthesis and three E. coli genes essential for the formation of a pimelate thioester, a key precursor of biotin synthesis. A yeast strain expressing these genes readily grew in biotin-free medium, irrespective of the presence of oxygen. However, the engineered strain exhibited lower specific growth rates in biotin-free media than in biotin-supplemented media. Following adaptive laboratory evolution in anaerobic cultures, evolved cell lines that no longer showed this growth difference were characterized by genome sequencing and proteome analyses. The evolved isolates exhibited several genomic rearrangements, including a whole-genome duplication, which caused alterations in the relative gene dosages of biosynthetic pathway genes. These alterations resulted in a reduced abundance of the enzymes catalyzing the first three steps of the E. coli biotin pathway. The evolved pathway configuration was reverse engineered in the diploid industrial S. cerevisiae strain Ethanol Red. The resulting strain grew at nearly the same rate in biotin-supplemented and biotin-free media. This study established the first genetic engineering strategy to enable biotin-independent anaerobic growth of S. cerevisiae and demonstrated its portability in industrial strain backgrounds.