The ribosomal protein Rps15p is required for nuclear exit of the 40S subunit precursors in yeast

Léger-Silvestre, Isabelle; Milkereit, Philipp; Ferreira-Cerca, Sébastien; Saveanu, Cosmin; Rousselle, Jean-Claude; Choesmel, Valérie; Guinefoleau, Cécile; Gas, Nicole; Gleizes, Pierre‐Emmanuel

doi:10.1038/sj.emboj.7600252

Cited by 101 publications

(143 citation statements)

References 37 publications

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“…Mutations in these genes have been reported in *55 % of DBA patients. The RPS19 protein plays an important role in 18S rRNA maturation in both yeast and human cells [5,6]. All the RPS19 mutations were found in heterozygosity with the wild-type sequence; this is consistent with the dominant inheritance pattern and with the evidence that the RPS19 knockout is lethal prior to implantation in mice [7].…”

supporting

confidence: 64%

A Novel Mutation of Ribosomal Protein S19 Gene in a Chinese Child with Diamond-Blackfan Anemia

Jiang

2015

Indian J Hematol Blood Transfus

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supporting

confidence: 64%

A Novel Mutation of Ribosomal Protein S19 Gene in a Chinese Child with Diamond-Blackfan Anemia

Jiang

2015

Indian J Hematol Blood Transfus

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“…Both Enp1 and Nob1 are late pre-40S-associated biogenesis factors that accumulate in the nucleus when export is blocked (Schafer et al 2003;Leger-Silvestre et al 2004;Strunk et al 2011). Enp1 is found in both 90S and pre-40S particles, and the GFPtagged protein is detected in both the nucleolus and the cytoplasm in exponentially growing cells (Schafer et al 2003;Leger-Silvestre et al 2004); Nob1 is associated with late pre-40S particles, and the GFP-tagged protein is predominantly cytoplasmic at steady state but redistributes to the nucleus upon inhibition of Crm1 (Schafer et al 2003;Zemp et al 2009). These biogenesis factors are a more sensitive measure of 40S export kinetics than RpS2 and RpS3 because they rapidly shuttle.…”

Section: Overexpression Of Ltv1dnes Affects Rps3 But Not Pre-40s Exportmentioning

confidence: 99%

Genetic Analysis of the Ribosome Biogenesis Factor Ltv1 ofSaccharomyces cerevisiae

et al. 2014

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Ribosome biogenesis has been studied extensively in the yeast Saccharomyces cerevisiae. Yeast Ltv1 is a conserved 40S-associated biogenesis factor that has been proposed to function in small subunit nuclear export. Here we show that Ltv1 has a canonical leucine-rich nuclear export signal (NES) at its extreme C terminus that is both necessary for Crm1 interaction and Ltv1 export. The C terminus of Ltv1 can substitute for the NES in the 60S-export adapter Nmd3, demonstrating that it is a functional NES. Overexpression of an Ltv1 lacking its NES (Ltv1ΔC13) was strongly dominant negative and resulted in the nuclear accumulation of RpS3-GFP; however, export of the pre-40S was not affected. In addition, expression of endogenous levels of Ltv1ΔC protein complemented both the slow-growth phenotype and the 40S biogenesis defect of an ltv1 deletion mutant. Thus, if Ltv1 is a nuclear export adapter for the pre-40S subunit, its function must be fully redundant with additional export factors. The dominant negative phenotype of Ltv1ΔNES overexpression was suppressed by co-overexpressing RpS3 and its chaperone, Yar1, or by deletion of the RpS3-binding site in Ltv1ΔNES, suggesting that titration of RpS3 by Ltv1ΔNES is deleterious in yeast. The dominant-negative phenotype did not correlate with a decrease in 40S levels but rather with a reduction in the polysome-to-monosome ratio, indicating reduced rates of translation. We suggest that titration of RpS3 by excess nuclear Ltv1 interferes with 40S function or with a nonribosomal function of RpS3.

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“…Tsr1 moved from the cytosol to the nucleolus after MMS treatment. This protein is required for processing 20S pre-rRNA in the cytoplasm and associates with pre-40S ribosomal particles (39). Dynamic localization of Tsr1 was also previously observed in cells depleted of ribosomal protein of the small subunit-15 (Rps15), a protein component of the 40S ribosomal subunit.…”

Section: Discussionmentioning

confidence: 75%

“…Dynamic localization of Tsr1 was also previously observed in cells depleted of ribosomal protein of the small subunit-15 (Rps15), a protein component of the 40S ribosomal subunit. Rps15 depletion leads to retention of 20S pre-rRNA-containing late pre-40S particles and its associating protein Tsr1 in the nucleolus (39). Given that MMS is a DNA-damaging agent and that it induces stalled replication forks (40), our data suggest that the MMS-induced DNA damage pathway is linked to ribosome biogenesis.…”

Section: Discussionmentioning

confidence: 87%

Proteome-wide remodeling of protein location and function by stress

Lee

Sung

Kim

et al. 2014

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

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Protein location and function can change dynamically depending on many factors, including environmental stress, disease state, age, developmental stage, and cell type. Here, we describe an integrative computational framework, called the conditional function predictor (CoFP; http://nbm.ajou.ac.kr/cofp/), for predicting changes in subcellular location and function on a proteome-wide scale. The essence of the CoFP approach is to cross-reference general knowledge about a protein and its known network of physical interactions, which typically pool measurements from diverse environments, against gene expression profiles that have been measured under specific conditions of interest. Using CoFP, we predict condition-specific subcellular locations, biological processes, and molecular functions of the yeast proteome under 18 specified conditions. In addition to highly accurate retrieval of previously known gold standard protein locations and functions, CoFP predicts previously unidentified condition-dependent locations and functions for nearly all yeast proteins. Many of these predictions can be confirmed using high-resolution cellular imaging. We show that, under DNA-damaging conditions, Tsr1, Caf120, Dip5, Skg6, Lte1, and Nnf2 change subcellular location and RNA polymerase I subunit A43, Ino2, and Ids2 show changes in DNA binding. Beyond specific predictions, this work reveals a global landscape of changing protein location and function, highlighting a surprising number of proteins that translocate from the mitochondria to the nucleus or from endoplasmic reticulum to Golgi apparatus under stress.dynamic function prediction | protein translocation | DTT and MMS | systems biology | bioinformatics A cellular response can induce striking changes in the subcellular location and function of proteins. As a recent example, the activating transcription factor-2 (ATF2) plays an oncogenic role in the nucleus, whereas genotoxic stress-induced localization within the mitochondria gives ATF2 the ability to play tumor suppressor, resulting in promotion of cell death (1). Changes in protein location are typically identified using a variety of experimental methods [e.g., protein tagging (2), immunolabeling (3), or cellular subfractionation of target organelles followed by mass spectrometry (4)]. Although highly successful, such measurements can be laborious and time-consuming, even for a single protein (all methods except mass spectrometry) and condition (all methods).For these reasons and others, computational prediction of protein location and function has been a very active area of bioinformatic research. Early methods attempted to infer protein function based mainly on individual protein features, such as sequence similarity or structural homology (3,(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17). These methods range from simple sequence-sequence comparisons to profile-or pattern-based supervised learning methods. Other methods predicted protein function using gene expression data (18, 19) based on the observation that proteins wit...

show abstract

The ribosomal protein Rps15p is required for nuclear exit of the 40S subunit precursors in yeast

Cited by 101 publications

References 37 publications

A Novel Mutation of Ribosomal Protein S19 Gene in a Chinese Child with Diamond-Blackfan Anemia

A Novel Mutation of Ribosomal Protein S19 Gene in a Chinese Child with Diamond-Blackfan Anemia

Genetic Analysis of the Ribosome Biogenesis Factor Ltv1 ofSaccharomyces cerevisiae

Proteome-wide remodeling of protein location and function by stress

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