Regulation of Glucose-Dependent Gene Expression by the RNA Helicase Dbp2 in Saccharomyces cerevisiae

Abstract

Cellular homeostasis requires a fine balance between energy uptake, utilization, and growth. Dbp2 is a member of the DEAD-box protein family in Saccharomyces cerevisiae with characterized ATPase and helicase activity in vitro. DEAD-box RNA helicases are a class of enzymes that utilize ATP hydrolysis to remodel RNA and/or RNA-protein (RNP) composition. Dbp2 has been proposed to utilize its helicase activity in vivo to promote RNA-protein complex assembly of both messenger (m)RNAs and long noncoding (lnc)RNAs. Previous work from our laboratory demonstrated that loss of DBP2 enhances the lncRNA-dependent transcriptional induction of the GAL genes by abolishing glucose-dependent repression. Herein, we report that either a carbon source switch or glucose deprivation results in rapid export of Dbp2 to the cytoplasm. Genome-wide RNA sequencing identified a new class of antisense hexose transporter transcripts that are specifically upregulated upon loss of DBP2. Further investigation revealed that both sense and antisense hexose transporter (HXT) transcripts are aberrantly expressed in DBP2-deficient cells and that this expression pathway can be partially mimicked in wild-type cells by glucose depletion. We also find that Dbp2 promotes ribosome biogenesis and represses alternative ATP-producing pathways, as loss of DBP2 alters the transcript levels of ribosome biosynthesis (snoRNAs and associated proteins) and respiration gene products. This suggests that Dbp2 is a key integrator of nutritional status and gene expression programs required for energy homeostasis.

period -1 encodes an ATP-dependent RNA helicase that influences nutritional compensation of the Neurospora circadian clock

“…Interestingly, prd-1 is reported to have normal temperature compensation (22) so the splice site mutation in prd-1 influences only nutritional compensation; however, prd-1 may not be highly informative in terms of the mechanism of compensation because of its pleiotropic nature. The yeast ortholog of PRD-1, Dbp2p, is a bona fide RNA helicase having documented physical or genetics interactions with 84 unique genes (www.yeastgenome.org/locus/S000005056/overview) and whose mutation affects the expression of nearly 3,000 transcripts (19). DBP2 is not essential in Saccharomyces and has been implicated in a wide variety of functions, ranging from non-sensemediated decay and rRNA processing (23), to RNA quality control, mRNA decay, mRNP assembly and export of polyadenylated RNA from the nucleus, suppression of transcription from cryptic sites, and promotion of antisense lnc RNAs (16,17,24).…”

“…These data suggested to us that glucose might influence the expression or localization of PRD-1. Additional support for this possibility comes from analysis of the Saccharomyces ortholog of prd-1, the DBP2 gene, by Tran and coworkers, who have found rapid depletion of DBP2 from the yeast nucleus after removal of glucose from cultures (19). To follow expression, cultures of WT and prd-1 were inoculated into Bird medium containing 0.1% glucose and grown 24 h to deplete the glucose.…”

LncRNAs: Bridging environmental sensing and gene expression

“…74 Strikingly, nuclear depletion of Dbp2 using the "anchor away" strategy 75 resulted in time-dependent accumulation of R-loops beginning at the 5 0 end of GAL1 and spreading across GAL1, GAL10 and through the 3 0 end of GAL7. 53 Removal of the lncRNAs through genomic deletion reduced R-loops at the 5 0 end of GAL1 and abolished detection of these structures across the rest of the GAL cluster locus.…”

“…1C). One possibility is that these R-loops are transient, allowing recruitment of transcriptional 74 and prevents the accumulation of R-loops at the GAL gene cluster 53 via the assembly of Dbp2-dependent lncRNA-protein complexes. 56 This allows the successful docking of the Cyc8/Tup1 co-repressor complex and subsequent repression.…”

“…(B) Carbon Source Switch During a switch from glucose to galactose, Dbp2 is actively relocalized to the cytoplasm via export through the nuclear pore complex (NPC). 74 This may alter lncRNP assembly and cause R-loop formation and spreading across the GAL cluster. R-loop formation likely interferes with binding of transcriptional repressors and the Cyc8/Tup1 corepressor complex, causing derepression of the GAL genes.…”