Inhibition of 5′ to 3′ mRNA degradation under stress conditions in Saccharomyces cerevisiae: from GCN4 to MET16

Bénard, Lionel

doi:10.1261/rna.5183804

Cited by 20 publications

(14 citation statements)

References 50 publications

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“…3). These results complement previous studies that have shown that in yeast, general mRNA turnover is slowed during amino acid starvation, salt stress, or sugar-induced osmotic stress, although whether deadenylation was affected in those cases was not examined (Bénard 2004;Greatrix and van Vuuren 2006;Todeschini et al 2006). Moreover, heat shock has also been reported to stabilize ARE-containing mRNAs in mammalian cells and to affect the decay and deadenylation of the Hsp70 mRNA in Drosophila (Dellavalle et al 1994;Laroia et al 1999;Zhao et al 2002).…”

Section: Discussionsupporting

confidence: 87%

“…brown and red curves). This suggests that stress can also inhibit, to some extent, either decapping or 59 to 39 degradation, which could be consistent with previous observations that amino acid starvation can inhibit 59 to 39 exonuclease activity (Bénard 2004).…”

Section: Stress Inhibits Both the Ccr4p/pop2p/notp And Pan2p/pan3p Desupporting

confidence: 92%

“…For example, response to UV-B exposure leads to stabilization of many short-lived mRNAs in mammalian cells (Gowrishankar et al 2006). Conversely, in yeast, mild heat shock promotes rapid degradation of mRNAs encoding the ribosomal proteins (Herruer et al 1988), while glucose starvation, amino acid starvation, or sugar-induced osmotic stress causes stabilization of at least some yeast mRNAs (Jona et al 2000;Bénard 2004;Greatrix and van Vuuren 2006). How these changes in mRNA stability are related to the corresponding changes in translation that are occurring during the same stress response is not known.…”

Section: Introductionmentioning

confidence: 99%

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Translation-independent inhibition of mRNA deadenylation during stress in Saccharomyces cerevisiae

Hilgers¹,

Teixeira²,

Parker³

2006

RNA

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Post-transcriptional control mechanisms play an important role in regulating gene expression during cellular responses to stress. For example, many stresses inhibit translation, and at least some stresses inhibit mRNA turnover in yeast and mammalian cells. We show that hyperosmolarity, heat shock, and glucose deprivation stabilize multiple mRNAs in yeast, primarily through inhibition of deadenylation. Although these stresses inhibit translation and promote the movement of mRNAs into P-bodies, we also observed inhibition of deadenylation in cycloheximide-treated cells as well as in a mutant strain where translation initiation is impaired. This argues that inhibition of poly(A)-shortening is independent of the translational state of the mRNAs and can occur when mRNAs are localized in polysomes or are not engaged in translation. Analysis of pan2D or ccr4D strains indicates that stress inhibits the function of both the Ccr4p/Pop2p/Notp and the Pan2p/Pan3p deadenylases. We suggest that under stress, simultaneous repression of translation and deadenylation allows cells to selectively translate mRNAs specific to the stress response, while retaining the majority of the cytoplasmic pool of mRNAs for later reuse and recovery from stress. Moreover, because various cellular stresses also inhibit deadenylation in mammalian cells, this mechanism is likely to be a conserved aspect of the stress response.

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Section: Discussionsupporting

confidence: 87%

Section: Stress Inhibits Both the Ccr4p/pop2p/notp And Pan2p/pan3p Desupporting

confidence: 92%

Section: Introductionmentioning

confidence: 99%

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Translation-independent inhibition of mRNA deadenylation during stress in Saccharomyces cerevisiae

Hilgers¹,

Teixeira²,

Parker³

2006

RNA

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“…4A, see the similar growth rate of xrn1⌬ or xrn1⌬gcn4⌬ strains). In the presence of salt, however, both the xrn1⌬ and the xrn1⌬ gcn4⌬ strains show similar growth rates to the wild type strain, suggesting that some adaptation has occurred, possibly through increased activity of the alternative 3Ј-5Ј degradation pathway (43). Inactivation of both the 5Ј-3Ј and the 3Ј-5Ј pathways has been shown to be lethal in yeast (44).…”

Section: Gcn4 Expression Limits Pap Accumulation Under Conditions Of mentioning

confidence: 99%

Sodium-induced GCN4 Expression Controls the Accumulation of the 5′ to 3′ RNA Degradation Inhibitor, 3′-Phosphoadenosine 5′-Phosphate

Todeschini¹,

Condon

Bénard

2006

Journal of Biological Chemistry

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Most cytoplasmic mRNAs are decapped and digested by the 5-3-exonuclease Xrn1p in Saccharomyces cerevisiae. The activity of Xrn1p is naturally inhibited in the presence of 3-phosphoadenosine 5-phosphate (pAp), a metabolite produced during sulfate assimilation that is quickly metabolized to AMP by the enzymatic activity of Hal2p. However, pAp accumulates and 5-3 degradation decreases in the presence of ions known to inhibit Hal2p activity, such as sodium or lithium. We have shown that yeast cells can better adapt to the presence of sodium than lithium because of their ability to reduce pAp accumulation by activating HAL2 expression in a Gcn4p-dependent response, a regulatory loop that is likely to be conserved in different yeast species. We have thus identified a new role for the transcriptional activity of Gcn4p in maintaining an active mRNA degradation pathway under conditions of sodium stress. Since deregulation of proteins involved in different metabolic pathways is observed in xrn1⌬ mutants, the maintenance of mRNA degradation capacity is likely to be important for the accurate and rapid adaptation of gene expression to salt stress.Although the study of gene regulation has traditionally focused on transcription as a major regulator of gene expression, it has recently become apparent that the post-transcriptional regulation of gene expression may play an equally important role (1). Xrn1p is a major player in this post-transcriptional control in yeast because it is responsible for the turnover of the majority of cytoplasmic mRNAs (2). This role is evident in both the general deadenylation-dependent mRNA decay (3, 4) and nonsense-mediated mRNA decay pathways (5). Xrn1p is not essential, but XRN1 deletion mutants grow slowly, and mutations in XRN1 are known to have pleiotropic effects (6). Since Xrn1p acts at the last step in mRNA turnover, after decapping, xrn1 mutants accumulate decapped intermediates (2) that can persist in polysomes (7,8). This defect is potentially detrimental to cellular fitness, through an inability to remove decapped transcripts from the translation machinery in a timely fashion. An analysis of global protein expression in xrn1⌬ mutant strains revealed both up-and down-regulation of different sets of proteins involved in several metabolic pathways (9). Such alterations in gene expression would certainly be problematic under conditions of environmental stress, when cells are required to establish a particular gene expression program for adaptation.It has been demonstrated that inhibition of 5Ј-3Ј-exoribonuclease activity by the metabolite, 3Ј-phosphoadenosine 5Ј-phosphate (pAp), 3 occurs in the presence of toxic ions such as sodium and lithium (10) (Fig. 1). pAp is produced during the assimilation of sulfate, an essential process in all living organisms. Sulfate assimilation in Saccharomyces cerevisiae is initiated by the production of adenosine 5Ј-phosphosulfate (ApS) from ATP and sulfate (11). Phosphorylation of ApS yields 3Ј-phosphoadenosine 5Ј-phosphosulfate (pApS), which is then redu...

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“…This enabled us to categorize canonical pathways and functionally related gene clusters according to preferentially synthesis-regulated or turnover-regulated. At present, very little is known about the role of posttranscriptional control, although mounting evidence supports its importance, e.g., under stress conditions (25)(26)(27). Based on this and our own data, it may be hypothesized that under certain conditions, posttranscriptional control may be favored to keep pace with specific needs such as timely and energetically economic control of (specifically localized) gene expression (28).…”

Section: Discussionmentioning

confidence: 71%

Microarray analysis of newly synthesized RNA in cells and animals

Kenzelmann

Maertens

Hergenhahn

et al. 2007

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

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Current methods to analyze gene expression measure steady-state levels of mRNA. To specifically analyze mRNA transcription, we have developed a technique that can be applied in vivo in intact cells and animals. Our method makes use of the cellular pyrimidine salvage pathway and is based on affinity-chromatographic isolation of thiolated mRNA. When combined with data on mRNA steady-state levels, this method is able to assess the relative contributions of mRNA synthesis and degradation/stabilization. It overcomes limitations associated with currently available methods such as mechanistic intervention that disrupts cellular physiology, or the inability to apply the techniques in vivo. Our method was first tested in serum response of cultured fibroblast cells and then applied to the study of renal ischemia reperfusion injury, demonstrating its applicability for whole organs in vivo. Combined with data on mRNA steady-state levels, this method provided a detailed analysis of regulatory mechanisms of mRNA expression and the relative contributions of RNA synthesis and turnover within distinct pathways, and identification of genes expressed at low abundance at the transcriptional level.newly transcribed RNA ͉ posttranscriptional regulation ͉ RNA degradation/stabilization I n response to environmental changes, cells alter their gene expression program. Eukaryotic gene expression is a complex process that is fine-tuned at different levels, such as transcription, turnover, and translation of mRNAs. Microarray-based measurements of steady-state mRNA levels do not distinguish between different regulatory processes. Both transcriptional and posttranscriptional regulation, however, can profoundly influence steady-state mRNA levels (1-4). To evaluate de novo transcription and the relative contributions of mRNA transcription and turnover, nuclear transcription run-on and its modifications have long been the methods of choice (4-6). These methods, however, are either inherently cell-invasive and/or are not compatible with the assay formats currently used to analyze global gene expression. To avoid mechanistic intervention that disrupts cellular physiology for example by cell permeabilization, we modified a method in which we take advantage of the cellular pyrimidine salvage pathway. Pyrimidine ribonucleotides may be de novo synthesized from simple molecules by energetically expensive multistep pathways. Alternatively, ribonucleotide pools are sustained by recycling of the basic components derived from their catabolism during normal RNA turnover, the socalled salvage pathway, a mechanism that is energetically less expensive. By this more favorable pathway, it is possible to label and selectively enrich newly transcribed (nascent) RNA molecules (NT-RNA; refs. 7-9) in vivo by incorporation of exogenous 4-thiouridine (s4U) and subsequent RNA purification by affinity chromatography. The RNA can then be further processed by standard protocols for hybridization to oligonucleotide microarrays. We refer to our method with the acronym NIAC-...

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Inhibition of 5′ to 3′ mRNA degradation under stress conditions in Saccharomyces cerevisiae: from GCN4 to MET16

Cited by 20 publications

References 50 publications

Translation-independent inhibition of mRNA deadenylation during stress in Saccharomyces cerevisiae

Translation-independent inhibition of mRNA deadenylation during stress in Saccharomyces cerevisiae

Sodium-induced GCN4 Expression Controls the Accumulation of the 5′ to 3′ RNA Degradation Inhibitor, 3′-Phosphoadenosine 5′-Phosphate

Microarray analysis of newly synthesized RNA in cells and animals

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