Metabolic engineering of the non-conventional yeast Pichia ciferrii for production of rare sphingoid bases

• Published in: Metabolic engineering Vol. 14; no. 4; pp. 412 - 426
• Main Authors: Börgel, Daniel, van den Berg, Marco, Hüller, Thomas, Andrea, Heiko, Liebisch, Gerhard, Boles, Eckhard, Schorsch, Christoph, van der Pol, Ruud, Arink, Anne, Boogers, Ilco, van der Hoeven, Rob, Korevaar, Kees, Farwick, Mike, Köhler, Tim, Schaffer, Steffen
• Format: Journal Article
• Language: English
• Published: Belgium Elsevier Inc 01.07.2012
• Subjects: Alkaline Ceramidase - genetics; Alkaline Ceramidase - metabolism; Cell culture; Ceramidase; Ceramide; Codon optimization; Codons; Cosmetics; Diacetyl; Enzymes; Fermentation; Metabolic engineering; Metabolic Engineering - methods; Metabolic pathways; Mixed Function Oxygenases - genetics; Mixed Function Oxygenases - metabolism; Oxidoreductases - genetics; Oxidoreductases - metabolism; Pharmaceuticals; Pichia; Pichia - enzymology; Pichia - genetics; Pichia ciferrii; Sphinganine; Sphingolipids; Sphingosine; Sphingosine - analogs & derivatives; Sphingosine - biosynthesis; Sphingosine - genetics; Metabolic engineering; Sphingolipids; Pichia ciferrii; Sphinganine; Sphingosine; Codon optimization
• ISSN: 1096-7176; 1096-7184
• DOI: 10.1016/j.ymben.2012.03.003

The study describes the identification of sphingolipid biosynthesis genes in the non-conventional yeast Pichia ciferrii, the development of tools for its genetic modification as well as their application for metabolic engineering of P. ciferrii with the goal to generate strains capable of producing the rare sphingoid bases sphinganine and sphingosine. Several canonical genes encoding ceramide synthase (encoded by PcLAG1 and PcLAF1), alkaline ceramidase (PcYXC1) and sphingolipid C-4-hydroxylase(PcSYR2), as well as structural genes for dihydroceramide Δ4-desaturase (PcDES1) and sphingolipid Δ8-desaturase (PcSLD1) were identified, indicating that P. ciferrii would be capable of synthesizing desaturated sphingoid bases, a property not ubiquitously found in yeasts. In order to convert the phytosphingosine-producing P. ciferrii wildtype into a strain capable of producing predominantly sphinganine, Syringomycin E-resistant mutants were isolated. A stable mutant almost exclusively producing high levels of acetylated sphinganine was obtained and used as the base strain for further metabolic engineering. A metabolic pathway required for the three-step conversion of sphinganine to sphingosine was implemented in the sphinganine producing P. ciferrii strain and subsequently enhanced by screening for the appropriate heterologous enzymes, improvement of gene expression and codon optimization. These combined efforts led to a strain capable of producing 240mgL−1 triacetyl sphingosine in shake flask, with tri- and diacetyl sphinganine being the main by-products. Lab-scale fermentation of this strain resulted in production of up to 890mgkg−1 triacetyl sphingosine. A third by-product was unequivocally identified as triacetyl sphingadienine. It could be shown that inactivation of the SLD1 gene in P. ciferrii efficiently suppresses triacetyl sphingadienine formation. Further improvement of the described P. ciferrii strains will enable a biotechnological route to produce sphinganine and sphingosine for cosmetic and pharmaceutical applications. ► Identification of sphingolipid biosynthesis genes in P. ciferrii. ► Isolation of a syringomycin-resistant strain producing predominantly sphinganine. ► Construction of an efficient sphingosine-producing P. ciferrii strain. ► Production of 0.9g acetylated sphingosine per liter in lab-scale fermentation. ► Suppression of by-product formation by inactivating the SLD1 gene.