Effects of DHH1 deletion on gene expression in C. albicans
Ontology highlight
ABSTRACT:
ORGANISM(S): Candida albicans
PROVIDER: GSE284543 | GEO | 2025/02/18
REPOSITORIES: GEO
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Project description:The impact of RNA structures in coding sequences (CDS) within mRNAs is poorly understood. Here
we identify a novel and highly conserved mechanism of translational control involving RNA structures within coding sequences and the DEAD-box helicase Dhh1. Using yeast genetics and
genome-wide ribosome profiling analyses we show that this mechanism, initially derived from studies
of the Brome Mosaic virus RNA genome, extends to yeast and human mRNAs highly enriched in
membrane and secreted proteins. All Dhh1-dependent mRNAs, viral and cellular, share key common
features. First, they contain long and highly structured CDSs, including a region located around 42 to
120 nucleotides after the translation initiation site, second, they are directly bound by Dhh1 with a
specific binding distribution and third, complementary experimental approaches suggest that they are
activated by Dhh1 at the translation initiation step. Our results show that ribosome translocation is not the only unwinding force of CDS and uncover a conserved layer of translational control that involve
RNA helicases and RNA folding within CDS providing novel opportunities for regulation of
membrane and secretome proteins.
2016-11-04 | GSE87892 | GEO
Project description:Previous experiments revealed that DHH1, a RNA helicase involved in the regulation of mRNA stability and translation, complemented the phenotype of a Saccharomyces cerevisiae mutant affected in the expression of genes coding for monocarboxylic-acids transporters, JEN1 and ADY2. In wild type cells, JEN1 expression had been shown to be undetectable in the presence of glucose or formic acid, and induced in the presence of lactate. In this work, we show that JEN1 mRNA accumulates in a dhh1 mutant, when formic acid was used as sole carbon source. Dhh1 interacts with the decapping activator Dcp1 and with the deadenylase complex. This led to the hypothesis that JEN1 expression is post-transcriptionally regulated by Dhh1 in formic acid. Analyses of JEN1 mRNAs decay in wild-type and dhh1 mutant strains confirmed this hypothesis. Microarray analyses of dhh1 mutant indicated that Dhh1 plays a large role in metabolic adaptation, suggesting that carbon source changes triggers a complex interplay between transcriptional and post-transcriptional effects. We compared gene expression between wild type and dhh1 deleted yeast strains grown either with formate or in glucose as sole carbon source. The experiments were replicated using biologically independant samples with dye swap. A total of four hybridizations were performed.
2014-09-08 | E-GEOD-60983 | biostudies-arrayexpress
Project description:We have examined the roles of yeast mRNA decapping-activators Pat1 and Dhh1 in repressing the translation and abundance of specific mRNAs in nutrient-replete cells using ribosome profiling, RNA-Seq, CAGE analysis of capped mRNAs, RNA Polymerase II ChIP-Seq, and TMT-mass spectrometry of mutants lacking one or both factors. Although the Environmental Stress Response (ESR) is activated in dhh1 and pat1 mutants, hundreds of non-ESR transcripts are elevated in a manner indicating cumulative repression by Pat1 and Dhh1 in WT. These mRNAs show reduced decapping and diminished transcription in the mutants, indicating that impaired mRNA turnover drives transcript derepression in cells lacking Dhh1 or Pat1. mRNA degradation stimulated by Dhh1/Pat1 is not dictated by poor translation nor enrichment for suboptimal codons. Pat1 and Dhh1 also collaborate to reduce translation and protein production from many mRNAs. Transcripts showing concerted translational repression by Pat1/Dhh1 include mRNAs involved in cell adhesion or utilization of the poor nitrogen source allantoin. Pat1/Dhh1 also repress numerous transcripts involved in respiration, catabolism of non-preferred carbon or nitrogen sources, or autophagy; and we obtained evidence for elevated respiration and autophagy in the mutants. Thus, Pat1 and Dhh1 function as post-transcriptional repressors of multiple pathways normally activated only during nutrient limitation.
2023-10-24 | PXD042990 | Pride
Project description:Previous experiments revealed that DHH1, a RNA helicase involved in the regulation of mRNA stability and translation, complemented the phenotype of a Saccharomyces cerevisiae mutant affected in the expression of genes coding for monocarboxylic-acids transporters, JEN1 and ADY2. In wild type cells, JEN1 expression had been shown to be undetectable in the presence of glucose or formic acid, and induced in the presence of lactate. In this work, we show that JEN1 mRNA accumulates in a dhh1 mutant, when formic acid was used as sole carbon source. Dhh1 interacts with the decapping activator Dcp1 and with the deadenylase complex. This led to the hypothesis that JEN1 expression is post-transcriptionally regulated by Dhh1 in formic acid. Analyses of JEN1 mRNAs decay in wild-type and dhh1 mutant strains confirmed this hypothesis. Microarray analyses of dhh1 mutant indicated that Dhh1 plays a large role in metabolic adaptation, suggesting that carbon source changes triggers a complex interplay between transcriptional and post-transcriptional effects.
2014-09-08 | GSE60983 | GEO
Project description:To investigate the role of cytoplasmic helicases in the decay of Xrn1-sensitive lncRNAs, we performed RNA-Seq in WT, ecm32-delta, ski2-delta, slh1-delta, dbp1-delta and dhh1-delta yeast cells.
2023-07-27 | GSE235553 | GEO
Project description:P-bodies (PB) are cytoplasmic RNP complexes that aggregate into foci when cells are exposed to stress. While the core components and stress response of PB and related RNP granules are conserved, it remains unclear how and why cells assemble mRNP complexes into granule foci during stress. We use mass spectrometry and antibody-based microarray to analyze proteins and RNA, respectively, that are immunoisolated with the core PB protein Dhh1-GFP. Analysis of the RNA associated with Dhh1-GFP immunoisolate reveals an enrichment of mitochondrial catalytic RNPs complex, suggesting a role for PB in mitochondrial RNA processing. RNA from 7 anti-GFP immunoisolations as well as total (input) RNA for each experiment was prepared. The seven samples include one mock IP from a strain containing GFP alone as well as 6 from Dhh1-GFP strains, two replicates from a (+) glucose condition and four replicates from a (-) glucose condition in which Dhh1-GFP forms cytoplasmic foci. 5ug of total RNA and 200ng IP RNA was hybridized to cutsom Agilent microarrays and detected using the S9.6 monoclonal antibody to RNA:DNA hybrids (ATCC clone ) and a Cy3 labeled anti-mouse secondary antibody.
2015-09-16 | E-GEOD-65989 | biostudies-arrayexpress
Project description:Degradation of many yeast mRNAs involves decapping by Dcp1:Dcp2. Previous studies on decapping activators Edc3 and Scd6 suggested limited roles in promoting mRNA decay in yeast cells. RNA-seq analysis of mutants lacking one or both proteins reveals that Scd6 and Edc3 have largely redundant activities in targeting numerous mRNAs for degradation, which are masked in the single mutants. These transcripts are frequently targeted by decapping activators Dhh1 and Pat1 and the evidence suggests that Scd6/Edc3 act interchangeably to recruit Dhh1 to Dcp2 independently of Pat1. Ribosome profiling shows that redundancy between Scd6 and Edc3 and their functional interactions with Dhh1 and Pat1 extends to translational repression of particular transcripts, including a cohort of poorly translated mRNAs displaying interdependent regulation by all four factors. Scd6/Edc3 also participate with Dhh1/Pat1 in post-transcriptional repression of proteins required for respiration and catabolism of non-optimal carbon sources, which are normally expressed only in limiting glucose. Simultaneously eliminating Scd6/Edc3 increases mitochondrial membrane potential and elevates metabolites of the tricarboxylic acid and glyoxylate cycles critical for growth at low glucose levels. Thus, Scd6/Edc3 act redundantly, in parallel with Dhh1 and in cooperation with Pat1, to adjust gene expression to nutrient availability by controlling mRNA decapping and decay.
2024-10-08 | GSE270789 | GEO
Project description:Ace2 transcription factor family genes are found in many fungal genomes and are required for regulation of expression of genes involved in cell separation. We used transcriptional profiling to identify the targets of Ace2 in Candida albicans, and we show that these include several cell wall components, such as glucanases and glycosylphosphatidylinositol-anchored proteins. Expression is downregulated in ace2 deletion mutants in both yeast and hyphal cells. In addition, deleting ace2 results in dramatic changes in expression of metabolic pathways. Expression of glycolytic enzymes is reduced, while expression of respiratory genes (including those involved in the tricarboxylic acid cycle, oxidative phosphorylation, and ATP synthesis) is increased. Similar changes occur in both yeast and hyphal cells. In contrast, genes required for acetyl-coenzyme A and lipid metabolism are upregulated in an ace2 deletion mutant grown predominantly as yeast cells but are downregulated in hyphae. These results suggest that in wild-type strains, Ace2 acts to increase glycolysis and reduce respiration. This is supported by the observation that deleting ace2 results in increased resistance to antimycin A, a drug that inhibits respiration. We also show that Ace2 is required for filamentation in response to low oxygen concentrations (hypoxia). We suggest that filamentation is induced in wild-type cells by reducing respiration (using low oxygen or respiratory drugs) and that mutants with increased respiratory activity fail to undergo filamentation under these conditions. This SuperSeries is composed of the SubSeries listed below.
2007-02-23 | GSE7105 | GEO
Project description:P-bodies (PB) are cytoplasmic RNP complexes that aggregate into foci when cells are exposed to stress. While the core components and stress response of PB and related RNP granules are conserved, it remains unclear how and why cells assemble mRNP complexes into granule foci during stress. We use mass spectrometry and antibody-based microarray to analyze proteins and RNA, respectively, that are immunoisolated with the core PB protein Dhh1-GFP. Analysis of the RNA associated with Dhh1-GFP immunoisolate reveals an enrichment of mitochondrial catalytic RNPs complex, suggesting a role for PB in mitochondrial RNA processing.
2015-09-16 | GSE65989 | GEO
Project description:Degradation of many yeast mRNAs involves decapping by Dcp1:Dcp2. Previous studies on decapping activators Edc3 and Scd6 suggested limited roles in promoting mRNA decay in yeast cells. RNA-seq analysis of mutants lacking one or both proteins reveals that Scd6 and Edc3 have largely redundant activities in targeting numerous mRNAs for degradation, which are masked in the single mutants. These transcripts are frequently targeted by decapping activators Dhh1 and Pat1 and the evidence suggests that Scd6/Edc3 act interchangeably to recruit Dhh1 to Dcp2 independently of Pat1. Ribosome profiling shows that redundancy between Scd6 and Edc3 and their functional interactions with Dhh1 and Pat1 extends to translational repression of particular transcripts, including a cohort of poorly translated mRNAs displaying interdependent regulation by all four factors. Scd6/Edc3 also participate with Dhh1/Pat1 in post-transcriptional repression of proteins required for respiration and catabolism of non-optimal carbon sources, which are normally expressed only in limiting glucose. Simultaneously eliminating Scd6/Edc3 increases mitochondrial membrane potential and elevates metabolites of the tricarboxylic acid and glyoxylate cycles critical for growth at low glucose levels. Thus, Scd6/Edc3 act redundantly, in parallel with Dhh1 and in cooperation with Pat1, to adjust gene expression to nutrient availability by controlling mRNA decapping and decay.
2024-10-08 | GSE270790 | GEO