Stm1 modulates translation after 80S formation in<i>Saccharomyces cerevisiae</i>

Balagopal, Vidya; Parker, Roy

doi:10.1261/rna.2677311

Cited by 64 publications

(72 citation statements)

References 33 publications

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“…This would explain how STM1, which modulates translation by regulating formation of the 80S subunit of ribosomes (Balagopal and Parker 2011), functions as a high copy suppressor of cdc13-1 (Hayashi and Murakami 2002). Similarly, the recovery of san1-Δ as a robust suppressor of cdc13-1 (Downey et al 2006;Addinall et al 2008) is consistent with a role for San1 in mediating degradation of misfolded nuclear proteins (Fredrickson et al 2011).…”

Section: Discussionmentioning

confidence: 99%

A Naturally Thermolabile Activity Compromises Genetic Analysis of Telomere Function in Saccharomyces cerevisiae

et al. 2012

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The core assumption driving the use of conditional loss-of-function reagents such as temperature-sensitive mutations is that the resulting phenotype(s) are solely due to depletion of the mutant protein under nonpermissive conditions. However, prior published data, combined with observations presented here, challenge the generality of this assumption at least for telomere biology: for both wild-type yeast and strains bearing null mutations in telomere protein complexes, there is an additional phenotypic consequence when cells are grown above 34°. We propose that this synthetic phenotype is due to a naturally thermolabile activity that confers a telomere-specific defect, which we call the Tmp 2 phenotype. This prompted a re-examination of commonly used cdc13-ts and stn1-ts mutations, which indicates that these alleles are instead hypomorphic mutations that behave as apparent temperaturesensitive mutations due to the additive effects of the Tmp 2 phenotype. We therefore generated new cdc13-ts reagents, which are nonpermissive below 34°, to allow examination of cdc13-depleted phenotypes in the absence of this temperature-dependent defect. A return-to-viability experiment following prolonged incubation at 32°, 34°, and 36°with one of these new cdc13-ts alleles argues that the accelerated inviability previously observed at 36°in cdc13-1 rad9-Δ mutant strains is a consequence of the Tmp 2 phenotype. Although this study focused on telomere biology, viable null mutations that confer inviability at 36°have been identified for multiple cellular pathways. Thus, phenotypic analysis of other aspects of yeast biology may similarly be compromised at high temperatures by pathway-specific versions of the Tmp 2 phenotype.T ELOMERE research in the budding yeast Saccharomyces cerevisiae has made substantial contributions for 30 years, starting with the cloning of yeast telomeres (Szostak and Blackburn 1982;Shampay et al. 1984) and the identification of the first mutant strains with altered telomere length (Carson and Hartwell 1985;Lustig and Petes 1986). Subsequent studies have identified numerous factors that contribute to yeast telomere function. Two key complexes are a telomerase complex (composed of the TLC1 RNA and the Est1, Est2, and Est3 proteins) that is responsible for elongating the G-rich strand of chromosome termini and a heterotrimeric complex that we have called the t-RPA complex (Gao et al. 2007), composed of the essential genes CDC13, STN1, and TEN1, which recruits telomerase to chromosome ends and also confers an essential protective function. In addition, numerous proteins share roles at telomeres and double-strand breaks (Tel1, the Mre11/Rad50/Xrs2 complex, and the Ku heterodimer are three examples), and a cohort of proteins negatively regulate telomere length (Rap1, Rif1, and Rif2, as well as components of DNA replication machinery). Genome-wide efforts have expanded this list with the inclusion of several hundred additional genes (Askree et al. 2004;Gatbonton et al. 2006) that impact telomere function e...

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Section: Discussionmentioning

confidence: 99%

A Naturally Thermolabile Activity Compromises Genetic Analysis of Telomere Function in Saccharomyces cerevisiae

et al. 2012

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“…It has been hypothesized to recruit an as-yet-unknown factor or factors to promote the rearrangement of the mRNP structure from a pro-translation/stability state into an anti-translation/decay state (Lee et al 2010). Given that Stm1 and the Pat1/Lsm-ring complex are involved in the repression of translation and promote mRNA decapping/decay (Marnef and Standart 2010;Balagopal and Parker 2011), we speculate that these proteins may be the undiscovered factors that Puf3 recruits to its target mRNAs to promote their degradation. Going beyond the known role of Puf3, we found novel RNAdependent interactions between Puf3 and proteins involved in repressing translation, suggesting that Puf3 may also repress the expression of its mRNA targets at the translational level.…”

Section: Identification and Validation Of Novel Rna-binding Proteinsmentioning

confidence: 95%

Quantitative proteomic analysis reveals concurrent RNA–protein interactions and identifies new RNA-binding proteins in Saccharomyces cerevisiae

et al. 2013

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A growing body of evidence supports the existence of an extensive network of RNA-binding proteins (RBPs) whose combinatorial binding affects the post-transcriptional fate of every mRNA in the cell-yet we still do not have a complete understanding of which proteins bind to mRNA, which of these bind concurrently, and when and where in the cell they bind. We describe here a method to identify the proteins that bind to RNA concurrently with an RBP of interest, using quantitative mass spectrometry combined with RNase treatment of affinity-purified RNA-protein complexes. We applied this method to the known RBPs Pab1, Nab2, and Puf 3. Our method significantly enriched for known RBPs and is a clear improvement upon previous approaches in yeast. Our data reveal that some reported protein-protein interactions may instead reflect simultaneous binding to shared RNA targets. We also discovered more than 100 candidate RBPs, and we independently confirmed that 77% (23/30) bind directly to RNA. The previously recognized functions of the confirmed novel RBPs were remarkably diverse, and we mapped the RNA-binding region of one of these proteins, the transcriptional coactivator Mbf1, to a region distinct from its DNA-binding domain. Our results also provided new insights into the roles of Nab2 and Puf 3 in post-transcriptional regulation by identifying other RBPs that bind simultaneously to the same mRNAs. While existing methods can identify sets of RBPs that interact with common RNA targets, our approach can determine which of those interactions are concurrent-a crucial distinction for understanding post-transcriptional regulation.

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“…For example, Dhh1, a member of the DEAD box family of ATPases, represses translation in vitro and its overexpression in cells inhibits translation and leads to the accumulation of cytoplasmic mRNP granules (Coller and Parker 2005;Swisher et al 2010;Carroll et al 2011). Similarly, Pat1, Scd6, and Stm1 (which affects the decapping of some mRNAs [Balagopal and Parker 2009]) repress translation both in vivo and in vitro (Pilkington and Parker 2008;Nissan et al 2010;Balagopal and Parker 2011). Decapping activators can inhibit translation at different steps.…”

Section: Key Proteins Promoting Decapping and Repressing Translation mentioning

confidence: 99%

P-Bodies and Stress Granules: Possible Roles in the Control of Translation and mRNA Degradation

Decker

Parker

2012

Cold Spring Harbor Perspectives in Biology

697

665

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The control of translation and mRNA degradation is important in the regulation of eukaryotic gene expression. In general, translation and steps in the major pathway of mRNA decay are in competition with each other. mRNAs that are not engaged in translation can aggregate into cytoplasmic mRNP granules referred to as processing bodies (P-bodies) and stress granules, which are related to mRNP particles that control translation in early development and neurons. Analyses of P-bodies and stress granules suggest a dynamic process, referred to as the mRNA Cycle, wherein mRNPs can move between polysomes, P-bodies and stress granules although the functional roles of mRNPassembly into higher order structures remain poorly understood. In this article, we review what is known about the coupling of translation and mRNA degradation, the properties of P-bodies and stress granules, and how assembly of mRNPs into larger structures might influence cellular function.

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Stm1 modulates translation after 80S formation inSaccharomyces cerevisiae

Cited by 64 publications

References 33 publications

A Naturally Thermolabile Activity Compromises Genetic Analysis of Telomere Function in Saccharomyces cerevisiae

A Naturally Thermolabile Activity Compromises Genetic Analysis of Telomere Function in Saccharomyces cerevisiae

Quantitative proteomic analysis reveals concurrent RNA–protein interactions and identifies new RNA-binding proteins in Saccharomyces cerevisiae

P-Bodies and Stress Granules: Possible Roles in the Control of Translation and mRNA Degradation

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