Advances and opportunities in gene editing and gene regulation technology for Yarrowia lipolytica

Abstract

Yarrowia lipolytica has emerged as a biomanufacturing platform for a variety of industrial applications. It has been demonstrated to be a robust cell factory for the production of renewable chemicals and enzymes for fuel, feed, oleochemical, nutraceutical and pharmaceutical applications. Metabolic engineering of this non-conventional yeast started through conventional molecular genetic engineering tools; however, recent advances in gene/genome editing systems, such as CRISPR–Cas9, transposons, and TALENs, has greatly expanded the applications of synthetic biology, metabolic engineering and functional genomics of Y. lipolytica. In this review we summarize the work to develop these tools and their demonstrated uses in engineering Y. lipolytica, discuss important subtleties and challenges to using these tools, and give our perspective on important gaps in gene/genome editing tools in Y. lipolytica.

Recent advances in domesticating non‐model microorganisms

“…Y. lipolytica is an oleaginous yeast, originally named for its ability to grow on lipids as a carbon source. Over the last 30 years, extensive tool development efforts have made this organism one of the better‐domesticated non‐model yeasts as well as led to impressive metabolic engineering outcomes 12,59 …”

“…Below, we highlight recent advances in gene editing of several prominent non-model yeasts. yeasts as well as led to impressive metabolic engineering outcomes 12,59. Y. lipolytica does not have an endogenous plasmid, but functional screening of Y. lipolytica genomic DNA fragments facilitated the discovery of ARS elements capable of plasmid maintenance, ARS18, and ARS6860 as well as YlARS1 and YlARS2 61.…”

Promoters for lipogenesis-specific downregulation in Yarrowia lipolytica

“… 2018 ; Ganesan et al . 2019 )). The promoter from the Y. lipolytica alkaline extracellular protease XPR2 gene, was one of the first promoters identified and is still widely used (Blanchin-Roland, Cordero Otero and Gaillardin 1994 ).…”

“…Yarrowia lipolytica is an attractive host organism for industrial production of biofuels and chemicals (Nicaud 2012 ; Ganesan et al . 2019 ; Miller and Alper 2019 ). It is a non-conventional oleaginous yeast that is Generally Regarded as Safe (GRAS) and is amenable to metabolic engineering thanks to the availability of its genome sequence and wide array of genetic tools.…”

Sugar Alcohols and Organic Acids Synthesis in Yarrowia lipolytica: Where Are We?

“…Y. lipolytica is also known for its ability to produce and secrete enzymes naturally such as the lipase lip2p, proteases and RNases at high quantities [1,4], but also a panoply of metabolites such as organic acids and sugar alcohols. The release of the 20 Mb of its genome in 2004, and subsequent development of efficient genome editing tools have enabled the development of metabolic engineering strategies for the production of recombinant proteins and metabolites of biotechnological interest [5][6][7]. These engineering strategies also aimed to endow Y. lipolytica with features for the catabolism of complex carbohydrates contained in organic wastes generated from industries or agricultural practices [8].…”