Metabolic Adaptation to Nutrients Involves Coregulation of Gene Expression by the RNA Helicase Dbp2 and the Cyc8 Corepressor in Saccharomyces cerevisiae

G3 : Genes - Genomes - Genetics
Siwen WangElizabeth J Tran

Abstract

Cells fine-tune their metabolic programs according to nutrient availability in order to maintain homeostasis. This is achieved largely through integrating signaling pathways and the gene expression program, allowing cells to adapt to nutritional change. Dbp2, a member of the DEAD-box RNA helicase family in Saccharomyces cerevisiae, has been proposed to integrate gene expression with cellular metabolism. Prior work from our laboratory has reported the necessity of DBP2 in proper gene expression, particularly for genes involved in glucose-dependent regulation. Here, by comparing differentially expressed genes in dbp2∆ to those of 700 other deletion strains from other studies, we find that CYC8 and TUP1, which form a complex and inhibit transcription of numerous genes, corepress a common set of genes with DBP2 Gene ontology (GO) annotations reveal that these corepressed genes are related to cellular metabolism, including respiration, gluconeogenesis, and alternative carbon-source utilization genes. Consistent with a direct role in metabolic gene regulation, loss of either DBP2 or CYC8 results in increased cellular respiration rates. Furthermore, we find that corepressed genes have a propensity to be associated with overlapping lon...Continue Reading

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Citations

Dec 7, 2018·Wiley Interdisciplinary Reviews. RNA·Zheng XingElizabeth J Tran
May 8, 2020·The Journal of Biological Chemistry·Zheng XingElizabeth J Tran
Feb 1, 2021·The Journal of Biological Chemistry·Zheng XingElizabeth J Tran

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Datasets Mentioned

BETA
GSE58097

Methods Mentioned

BETA
RNA-seq
PCR
immunoprecipitation
Assay
ChIP

Software Mentioned

EdgeR
ImageQuant
SHort Read Mapping Program 2 ( SHRiMP2
Tophat
BioVenn
GenomicAlignments
Bowtie2
Bioconductor
DAVID
R

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