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Proteomic and transcriptomic analyses of Dhh1 complexes reveals mitochondrial RNP complex association with yeast P-bodies

ABSTRACT: 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.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE65989 | GEO | 2015/09/16

SECONDARY ACCESSION(S): PRJNA275648

REPOSITORIES: GEO

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Proteomic and transcriptomic analyses of Dhh1 complexes reveals mitochondrial RNP complex association with yeast P-bodies

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

Transcriptome analyses of dhh1 mutants in yeast

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

Transcriptome analyses of dhh1 mutants in yeast

2014-09-08 | E-GEOD-60983 | biostudies-arrayexpress

Ribosome profiling of dhh1∆ yeast

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

Saccharomyces cerevisiae

Project description:Proteomic and transcriptomic analyses of Dhh1 complexes reveals mitochondrial RNP complex association with yeast P-bodies

| PRJNA275648 | ENA

Regulation of transcript abundance and translationny decapping activators Pat1 and Dhh1

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

DHH1/DDX6-like RNA helicases maintain ephemeral half-lives of stress-response mRNAs

Project description:Gene transcription is counterbalanced by mRNA decay processes that regulate transcript quality and quantity. We show here that the evolutionarily conserved DHH1/DDX6-like RNA HELICASEs of Arabidopsis thaliana control the ephemerality of a subset of cellular mRNAs. These RNA helicases co-localize with key markers of processing bodies and stress granules and contribute to their subcellular dynamics. They function to limit the precocious accumulation and translation of stress-responsive mRNAs associated with autoimmunity and growth inhibition under non-stress conditions. Given the conservation of this RH subfamily, they may control basal levels of conditionally-regulated mRNAs in diverse eukaryotes, accelerating responses without penalty.

2020-04-29 | GSE136713 | GEO

Transcription profiling of Trypanosoma bruceii DHH1 wild type from pLEW100 for 24 hours

Project description:Induction of the expression of the DHH1 wild type from pLEW100 for 24 hours (M-1 24 hours Tetracycline). Non-induced cells were used as control.

2010-01-01 | E-MEXP-2025 | biostudies-arrayexpress

Transcription profiling of Trypanosoma brucei DHH1 DEAD:DQAD mutant from pLEW100 for 24 hours

Project description:Induction of the expression of the DHH1 DEAD:DQAD mutant from pLEW100 for 24 hours (thus, M-1 24 hours <br>Tetracycline). Uninduced cells were used as control.

2010-01-01 | E-MEXP-2026 | biostudies-arrayexpress

Xrn1-sensitive lncRNAs are globally insensitive to the cytoplasmic helicases Ecm32, Ski2, Slh1, Dbp1 and Dhh1

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

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