Oleaginous yeast biology elucidated with comparative genomics and transcriptomics | Poster Board #1104

Connecting genotype to phenotype in nonconventional yeasts can explain poorly understood traits and provide information needed to improve cell factories. In this study, we compare two strains of Kluyveromyces marxianus to gain insight into the thermotolerance, biosynthetic capacity, and transformation competence of this bioindustrially relevant species. To connect genotype to phenotype, we apply comparative genomics and machine learning guided coexpression analysis. Previous work by others has shown that K. marxianus is extremely thermotolerant, which makes it attractive for large scale fermentations where heat removal is inefficient, and has natural overproduction of platform metabolites like fatty acids, which can be converted to biofuels and other products. Recently, it was also reported that transformations with strain Km17 [ATCC 8635] yield 100 times more transformants than the type strain [ATCC56497]. To begin our investigation, we first sequenced the genome of K. marxianus Km17 with our previously reported Prymetime tool and compared it to the type strain. One orthogroup was found uniquely in Km17 and not the type strain, suggesting this orthogroup may be important for Km17’s transformation competence. Then, we analyzed the gene expression patterns of km17 under heat stress. We found that under heat stress, km17 upregulates biotin metabolism, amino acid transporters, and carbohydrate transporters and downregulates coenzyme and inorganic ion transporters. This indicates that transporter expression plays a key role in heat tolerance, which is usually the case for molecules and ions. To contextualize the general stress response of km17 among yeasts, we compared km17 gene expression response to salt stress, iron starvation, and nitrogen starvation conditions to other nonconventional yeasts we have previously analyzed (Yarrowia lipolytica, Debaryomyces hansenii, and Debaryomyces subglobosus). We found salt stress was not as impactful to the Km17 transcriptome as it is to Debaryomyces, yet the transcriptome did change significantly under nitrogen starvation and heat stress like Yarrowia lipolytica. This information provides key insights into understanding important cell factory characteristics like transformation efficiency, heat tolerance, and biosynthesis under stress. Our analysis also hints at generalizable genetic traits that can be used to identify potential cell factories among the growing number of isolated and identified yeast species.