Oleaginous Yeast Biology Elucidated With Comparative Transcriptomics.

Autor: Weintraub SJ; Department of Bioinformatics and Computational Biology, Worcester Polytechnic Institute, Worcester, Massachusetts, USA., Li Z; Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, Massachusetts, USA., Nakagawa CL; Department of Bioinformatics and Computational Biology, Worcester Polytechnic Institute, Worcester, Massachusetts, USA., Collins JH; Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, Massachusetts, USA., Young EM; Department of Bioinformatics and Computational Biology, Worcester Polytechnic Institute, Worcester, Massachusetts, USA.; Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, Massachusetts, USA.; Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts, USA.
Jazyk: angličtina
Zdroj: Biotechnology and bioengineering [Biotechnol Bioeng] 2024 Dec 10. Date of Electronic Publication: 2024 Dec 10.
DOI: 10.1002/bit.28891
Abstrakt: Extremophilic yeasts have favorable metabolic and tolerance traits for biomanufacturing- like lipid biosynthesis, flavinogenesis, and halotolerance - yet the connection between these favorable phenotypes and strain genotype is not well understood. To this end, this study compares the phenotypes and gene expression patterns of biotechnologically relevant yeasts Yarrowia lipolytica, Debaryomyces hansenii, and Debaryomyces subglobosus grown under nitrogen starvation, iron starvation, and salt stress. To analyze the large data set across species and conditions, two approaches were used: a "network-first" approach where a generalized metabolic network serves as a scaffold for mapping genes and a "cluster-first" approach where unsupervised machine learning co-expression analysis clusters genes. Both approaches provide insight into strain behavior. The network-first approach corroborates that Yarrowia upregulates lipid biosynthesis during nitrogen starvation and provides new evidence that riboflavin overproduction in Debaryomyces yeasts is overflow metabolism that is routed to flavin cofactor production under salt stress. The cluster-first approach does not rely on annotation; therefore, the coexpression analysis can identify known and novel genes involved in stress responses, mainly transcription factors and transporters. Therefore, this work links the genotype to the phenotype of biotechnologically relevant yeasts and demonstrates the utility of complementary computational approaches to gain insight from transcriptomics data across species and conditions.
(© 2024 Wiley Periodicals LLC.)
Databáze: MEDLINE
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