Transcriptomics elucidates metabolic regulation and functional promoters in the basidiomycete red yeast Xanthophyllomyces dendrorhous CBS 6938

Emma E. Tobin, Joseph H. Collins, Celeste B. Marsan, Gillian T. Nadeau, Kim Mori, Anna Lipzen, Stephen Mondo, Igor V. Grigoriev, Eric M. Young

Genomics has become the primary way to explore microbial diversity, because genetic tools are currently difficult to develop in non-model organisms. Here, we demonstrate that -omics can be leveraged to accelerate genetic tool development for the basidiomycete yeast Xanthophyllomyces dendrorhous CBS 6938, the sole biotechnologically relevant organism in the Tremellomycete family. First, we sequence the genome. Then, we perform transcriptomics under a variety of conditions, focusing on light and oxidative stress. This data not only reveals novel photobiology and metabolic regulation, it also allows derivation of constitutive and regulated gene expression parts. Our analysis of X. dendrorhous photobiology shows for the first time that a complex system of white-collar and cryptochrome homologs mediate response to ultraviolet light (UV). Our analysis of metabolic regulation shows that UV activates DNA repair, aromatic amino acid and carotenoid biosynthesis and represses central carbon metabolism and the fungal-like apoptotic pathway. Thus, X. dendrorhous shows a dynamic response toward biosynthetic pathways for light-absorbing compounds and survival and away from energy production. We then define a modular cloning system, including antibiotic selections, integration sites, and reporter genes, and use the transcriptomics to derive strong constitutive and regulated promoters. Notably, we discover a novel promoter from a hypothetical gene that has 9-fold activation upon UV exposure. Thus, -omics-to-parts workflows can simultaneously provide useful genomic data and advance genetic tools for non-model microbes, particularly those without a closely related model organism. This approach will be broadly useful in current efforts to engineer diverse microbes.