<i>S. cerevisiae</i> Vts1p induces deadenylation-dependent transcript degradation and interacts with the Ccr4p-Pop2p-Not deadenylase complex

Rendl, Laura M.; Bieman, Melissa A.; Smibert, Craig

doi:10.1261/rna.955508

Cited by 37 publications

(42 citation statements)

References 41 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Vts1 is a member of the Smaug (Smg) family of posttranscriptional RBPs which bind RNA through a conserved sterile alpha motif (SAM) that interacts with Smg recognition element (SRE)-containing transcripts (79,80). Vts1 recruits the CCR4-NOT deadenylase complex to SRE-containing mRNAs to initiate their degradation (67). In addition, Vts1 interacts with an eIF4E-interacting protein, Eap1, which represses mRNA translation in S. cerevisiae (68).…”

Section: Discussionmentioning

confidence: 99%

“…enriched over the genome for 3=-UTRs having at least one instance of any of the RBP motif sets. Vts1 is an RBP involved in mRNA decay and repression (67,68). Because the Vts1 motif was the enriched match most frequently found in the SNF1-dependent transcript sequences, we examined its expression in published data sets to determine whether its expression might be correlated with their decay.…”

Section: Figmentioning

confidence: 99%

See 1 more Smart Citation

Snf1-Dependent Transcription Confers Glucose-Induced Decay upon the mRNA Product

Braun

Dombek

Young

2016

Molecular and Cellular Biology

View full text Add to dashboard Cite

In the yeast Saccharomyces cerevisiae, the switch from respiratory metabolism to fermentation causes rapid decay of transcripts encoding proteins uniquely required for aerobic metabolism. Snf1, the yeast ortholog of AMP-activated protein kinase, has been implicated in this process because inhibiting Snf1 mimics the addition of glucose. In this study, we show that the SNF1-dependent ADH2 promoter, or just the major transcription factor binding site, is sufficient to confer glucose-induced mRNA decay upon heterologous transcripts. SNF1-independent expression from the ADH2 promoter prevented glucose-induced mRNA decay without altering the start site of transcription. SNF1-dependent transcripts are enriched for the binding motif of the RNA binding protein Vts1, an important mediator of mRNA decay and mRNA repression whose expression is correlated with decreased abundance of SNF1-dependent transcripts during the yeast metabolic cycle. However, deletion of VTS1 did not slow the rate of glucose-induced mRNA decay. ADH2 mRNA rapidly dissociated from polysomes after glucose repletion, and sequences bound by RNA binding proteins were enriched in the transcripts from repressed cells. Inhibiting the protein kinase A pathway did not affect glucose-induced decay of ADH2 mRNA. Our results suggest that Snf1 may influence mRNA stability by altering the recruitment activity of the transcription factor Adr1. T he regulation of gene expression by nutritional conditions inSaccharomyces cerevisiae yeast, particularly the availability of glucose, has been a paradigm of transcriptional control (1-7). Glucose deprivation leads to a global reorganization of transcription (8). Numerous genes are upregulated to allow the cell to switch to a respiratory mode of metabolism, and a large number of genes are downregulated as the cells adapt to a lower rate of growth. Snf1, the yeast ortholog of AMP-activated protein kinase (AMPK) (6), is responsible for upregulating the expression of over 400 genes after glucose depletion (9). Snf1, together with the cyclic AMP (cAMP)-dependent protein kinase A (PKA) and target of rapamycin (TOR) pathways, coordinates many of the nutrientresponsive metabolic pathways in yeast (10). Despite the preponderance of evidence indicating altered transcription as the major factor determining the increase in mRNA abundance when yeast cells are depleted of glucose, there is considerable evidence indicating that posttranscriptional changes, particularly an increase in mRNA stability, are also important in determining gene expression levels (11)(12)(13)(14)(15). A recent study demonstrated that promoter sequences influence the subcellular location and efficiency of translation of transcripts upregulated by glucose starvation (16). Thus, promoter sequences appear to have a role in gene expression that includes both transcriptional and posttranscriptional processes.Glucose-induced mRNA decay is a process that leads to rapid loss of mRNAs encoding enzymes required for efficient aerobic respiration when glucose is replenished. ...

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Figmentioning

confidence: 99%

Snf1-Dependent Transcription Confers Glucose-Induced Decay upon the mRNA Product

Braun

Dombek

Young

2016

Molecular and Cellular Biology

View full text Add to dashboard Cite

show abstract

“…For example, deadenylation by the complex is involved in post-transcriptional control during oogenesis and embryonic development in Drosophila (Morris et al 2005;Semotok et al 2005;Zaessinger et al 2006;Chicoine et al 2007;Kadyrova et al 2007). The deadenylase can be directed toward specific mRNAs by association with RNA binding proteins such as the PUF proteins (Goldstrohm et al 2006) or Drosophila Smaug and its yeast homolog Vts1p (Aviv et al 2003;Semotok et al 2005;Zaessinger et al 2006;Rendl et al 2008). Alternatively, miRNAs can be responsible for the recruitment of the CCR4-NOT complex to specific mRNAs (Behm-Ansmant et al 2006;Fabian et al 2009).…”

Section: Introductionmentioning

confidence: 99%

Subunits of the Drosophila CCR4-NOT complex and their roles in mRNA deadenylation

Temme¹,

Zhang²,

Kremmer³

et al. 2010

RNA

151

198

View full text Add to dashboard Cite

The CCR4-NOT complex is the main enzyme catalyzing the deadenylation of mRNA. We have investigated the composition of this complex in Drosophila melanogaster by immunoprecipitation with a monoclonal antibody directed against NOT1. The CCR4, CAF1 (=POP2), NOT1, NOT2, NOT3, and CAF40 subunits were associated in a stable complex, but NOT4 was not. Factors known to be involved in mRNA regulation were prominent among the other proteins coprecipitated with the CCR4-NOT complex, as analyzed by mass spectrometry. The complex was localized mostly in the cytoplasm but did not appear to be a major component of P bodies. Of the known CCR4 paralogs, Nocturnin was found associated with the subunits of the CCR4-NOT complex, whereas Angel and 3635 were not. RNAi experiments in Schneider cells showed that CAF1, NOT1, NOT2, and NOT3 are required for bulk poly(A) shortening and hsp70 mRNA deadenylation, but knock-down of CCR4, CAF40, and NOT4 did not affect these processes. Overexpression of catalytically dead CAF1 had a dominant-negative effect on mRNA decay. In contrast, overexpression of inactive CCR4 had no effect. We conclude that CAF1 is the major catalytically important subunit of the CCR4-NOT complex in Drosophila Schneider cells. Nocturnin may also be involved in mRNA deadenylation, whereas there is no evidence for a similar role of Angel and 3635.

show abstract

“…We applied our method to characterize the interactions of the conserved RNA binding domain of a sequence-and structure-specific RBP (Vts1 in Saccharomyces cerevisiae; Smaug in metazoans). We chose to study Vts1 because of its biological significance as a key regulator of RNA stability in development (20) and because decades of prior study provided a gold standard against which to benchmark our results (21)(22)(23)(24)(25)(26)(27).…”

mentioning

confidence: 99%

Comprehensive and quantitative mapping of RNA–protein interactions across a transcribed eukaryotic genome

She

Chakravarty

Layton

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

108

View full text Add to dashboard Cite

RNA-binding proteins (RBPs) control the fate of nearly every transcript in a cell. However, no existing approach for studying these posttranscriptional gene regulators combines transcriptomewide throughput and biophysical precision. Here, we describe an assay that accomplishes this. Using commonly available hardware, we built a customizable, open-source platform that leverages the inherent throughput of Illumina technology for direct biophysical measurements. We used the platform to quantitatively measure the binding affinity of the prototypical RBP Vts1 for every transcript in the Saccharomyces cerevisiae genome. The scale and precision of these measurements revealed many previously unknown features of this well-studied RBP. Our transcribed genome array (TGA) assayed both rare and abundant transcripts with equivalent proficiency, revealing hundreds of low-abundance targets missed by previous approaches. These targets regulated diverse biological processes including nutrient sensing and the DNA damage response, and implicated Vts1 in de novo gene "birth." TGA provided single-nucleotide resolution for each binding site and delineated a highly specific sequence and structure motif for Vts1 binding. Changes in transcript levels in vts1Δ cells established the regulatory function of these binding sites. The impact of Vts1 on transcript abundance was largely independent of where it bound within an mRNA, challenging prevailing assumptions about how this RBP drives RNA degradation. TGA thus enables a quantitative description of the relationship between variant RNA structures, affinity, and in vivo phenotype on a transcriptome-wide scale. We anticipate that TGA will provide similarly comprehensive and quantitative insights into the function of virtually any RBP.RNA | next-generation sequencing | systems biochemistry | RNA binding proteins | Vts1 R NA-binding proteins (RBPs) constitute 5-10% of the eukaryotic proteome (1-3) and collectively govern the localization, translation, and decay of virtually every transcript (4-6). Despite the ubiquity of RBPs and their central importance in gene regulation, decoding the links between RNA primary sequence and its cadre of regulators remains a major unresolved challenge (7). Current approaches for characterizing RBP function generally involve trade-offs between throughput, comprehensiveness, and quantitative precision. Biophysical measurements can be made with targeted biochemical approaches such as electrophoretic mobility shift assays (EMSAs) or fluorescence polarization (FP) (8, 9), but these methods can only interrogate known RNA-protein interactions and are inherently lowthroughput. Selection-based approaches [e.g., in vitro selection, high-throughput sequencing of RNA, and sequence-specificity landscapes (SEQRS)/RNA bind-n-seq (RBNS)] achieve higher throughput, but these techniques remove binding sites from their natural sequence context and identify "winners" based on more than simple affinity (10). Transcriptome-wide methods, which often use cross-linking and immunoprecipi...

show abstract

S. cerevisiae Vts1p induces deadenylation-dependent transcript degradation and interacts with the Ccr4p-Pop2p-Not deadenylase complex

Cited by 37 publications

References 41 publications

Snf1-Dependent Transcription Confers Glucose-Induced Decay upon the mRNA Product

Snf1-Dependent Transcription Confers Glucose-Induced Decay upon the mRNA Product

Subunits of the Drosophila CCR4-NOT complex and their roles in mRNA deadenylation

Comprehensive and quantitative mapping of RNA–protein interactions across a transcribed eukaryotic genome

Contact Info

Product

Resources

About