scholarly journals Nuclear Pre-mRNA Decapping and 5′ Degradation in Yeast Require the Lsm2-8p Complex

2004 ◽  
Vol 24 (21) ◽  
pp. 9646-9657 ◽  
Author(s):  
Joanna Kufel ◽  
Cecile Bousquet-Antonelli ◽  
Jean D. Beggs ◽  
David Tollervey
Keyword(s):  
Heat Shock ◽  
Mrna Export ◽  
Mrna Degradation ◽  
Mrna Decapping ◽  
Nuclear Rna ◽  
Mrna Analysis ◽  
Degradation Intermediates

ABSTRACT Previous analyses have identified related cytoplasmic Lsm1-7p and nuclear Lsm2-8p complexes. Here we report that mature heat shock and MET mRNAs that are trapped in the nucleus due to a block in mRNA export were strongly stabilized in strains lacking Lsm6p or the nucleus-specific Lsm8p protein but not by the absence of the cytoplasmic Lsm1p. These nucleus-restricted mRNAs remain polyadenylated until their degradation, indicating that nuclear mRNA degradation does not involve the incremental deadenylation that is a key feature of cytoplasmic turnover. Lsm8p can be UV cross-linked to nuclear poly(A)+ RNA, indicating that an Lsm2-8p complex interacts directly with nucleus-restricted mRNA. Analysis of pre-mRNAs that contain intronic snoRNAs indicates that their 5′ degradation is specifically inhibited in strains lacking any of the Lsm2-8p proteins but Lsm1p. Nucleus-restricted mRNAs and pre-mRNA degradation intermediates that accumulate in lsm mutants remain 5′ capped. We conclude that the Lsm2-8p complex normally targets nuclear RNA substrates for decapping.

scholarly journals Capped mRNA Degradation Intermediates Accumulate in the Yeast spb8-2 Mutant

1998 ◽  
Vol 18 (9) ◽  
pp. 5062-5072 ◽  
Author(s):  
Ronald Boeck ◽  
Bruno Lapeyre ◽  
Christine E. Brown ◽  
Alan B. Sachs
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Family Member ◽  
Gene Deletion ◽  
Binding Protein ◽  
Mrna Degradation ◽  
Protein Family ◽  
Suppressor Mutation ◽  
Mrna Decapping ◽  
Mrna Species ◽  
Degradation Intermediates

ABSTRACT mRNA in the yeast Saccharomyces cerevisiae is primarily degraded through a pathway that is stimulated by removal of the mRNA cap structure. Here we report that a mutation in the SPB8(YJL124c) gene, initially identified as a suppressor mutation of a poly(A)-binding protein (PAB1) gene deletion, stabilizes the mRNA cap structure. Specifically, we find that thespb8-2 mutation results in the accumulation of capped, poly(A)-deficient mRNAs. The presence of this mutation also allows for the detection of mRNA species trimmed from the 3′ end. These data show that this Sm-like protein family member is involved in the process of mRNA decapping, and they provide an example of 3′-5′ mRNA degradation intermediates in yeast.

scholarly journals Differential expression of LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated in human epithelial ovarian cancer.

2021 ◽  
Author(s):  
Shahan Mamoor
Keyword(s):  
Ovarian Cancer ◽  
Epithelial Ovarian Cancer ◽  
Fallopian Tube ◽  
Expression Profiles ◽  
Mrna Degradation ◽  
High Grade ◽  
Small Nuclear Rna ◽  
Primary Tumors ◽  
Ovarian Cancers ◽  
Nuclear Rna

Epithelial ovarian cancer (EOC) is the most lethal gynecologic cancer (1). We performed discovery of genes associated with epithelial ovarian cancer and of the high-grade serous ovarian cancer (HGSC) subtype, using published microarray data (2, 3) to compare global gene expression profiles of normal ovary or fallopian tube with that of primary tumors from women diagnosed with epithelial ovarian cancer or HGSC. We identified the gene encoding LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated, LSM4, as among the genes whose expression was most different in epithelial ovarian cancer as compared to the normal fallopian tube. LSM4 expression was significantly higher in high-grade serous ovarian tumors relative to normal fallopian tube. LSM4 expression correlated with overall survival in patients with ovarian cancer. These data indicate that expression of LSM4 is perturbed in epithelial ovarian cancers broadly and in ovarian cancers of the HGSC subtype. LSM4 may be relevant to pathways underlying ovarian cancer initiation (transformation) or progression.

scholarly journals The Mitogen-Activated Protein Kinase Slt2 Regulates Nuclear Retention of Non-Heat Shock mRNAs during Heat Shock-Induced Stress

2010 ◽  
Vol 30 (21) ◽  
pp. 5168-5179 ◽  
Author(s):  
Sean R. Carmody ◽  
Elizabeth J. Tran ◽  
Luciano H. Apponi ◽  
Anita H. Corbett ◽  
Susan R. Wente
Keyword(s):  
Heat Shock ◽  
Map Kinase ◽  
Mrna Export ◽  
Mitogen Activated Protein Kinase ◽  
Focus Formation ◽  
Mrna Accumulation ◽  
Heat Shock Stress ◽  
Mitogen Activated Protein ◽  
Nuclear Foci ◽  
Shock Stress

ABSTRACT Cellular adaptation to environmental stress conditions requires rapid and specific changes in gene expression. During heat shock, most polyadenylated mRNAs are retained in the nucleus, whereas the export of heat shock-induced mRNAs is allowed. Although essential mRNA export factors are known, the precise mechanism for regulating transport is not fully understood. Here we find that during heat shock in Saccharomyces cerevisiae, the mRNA-binding protein Nab2 is phosphorylated on threonine 178 and serine 180 by the mitogen-activated protein (MAP) kinase Slt2/Mpk1. Slt2 is required for nuclear poly(A+) mRNA accumulation upon heat shock, and thermotolerance is decreased in a nup42 nab2-T178A/S180A mutant. Coincident with phosphorylation, Nab2 and Yra1 colocalize in nuclear foci with Mlp1, a protein involved in mRNA retention. Nab2 nuclear focus formation and Nab2 phosphorylation are independent, suggesting that heat shock induces multiple cellular alterations that impinge upon transport efficiency. Under normal conditions, we find that the mRNA export receptor Mex67 and Nab2 directly interact. However, upon heat shock stress, Mex67 does not localize to the Mlp1 nuclear foci, and its association with Nab2 complexes is reduced. These results reveal a novel mechanism by which the MAP kinase Slt2 and Mlp1 control mRNA export factors during heat shock stress.

scholarly journals dTIS11 Protein-dependent Polysomal Deadenylation Is the Key Step in AU-rich Element-mediated mRNA Decay in Drosophila Cells

2012 ◽  
Vol 287 (42) ◽  
pp. 35527-35538 ◽  
Author(s):  
Caroline Vindry ◽  
Aurélien Lauwers ◽  
David Hutin ◽  
Romuald Soin ◽  
Corinne Wauquier ◽  
...  
Keyword(s):  
Antimicrobial Peptide ◽  
Molecular Mechanism ◽  
Mrna Decay ◽  
Degradation Process ◽  
Mrna Degradation ◽  
Decay Process ◽  
Human Protein ◽  
P Bodies ◽  
Drosophila Cells ◽  
Degradation Intermediates

The destabilization of AU-rich element (ARE)-containing mRNAs mediated by proteins of the TIS11 family is conserved among eukaryotes including Drosophila. Previous studies have demonstrated that Tristetraprolin, a human protein of the TIS11 family, induces the degradation of ARE-containing mRNAs through a large variety of mechanisms including deadenylation, decapping, and P-body targeting. We have previously shown that the degradation of the mRNA encoding the antimicrobial peptide Cecropin A1 (CecA1) is controlled by the TIS11 protein (dTIS11) in Drosophila cells. In this study, we used CecA1 mRNA as a model to investigate the molecular mechanism of dTIS11-mediated mRNA decay. We observed that during the biphasic deadenylation and decay process of this mRNA, dTIS11 enhances deadenylation performed by the CCR4-CAF-NOT complex while the mRNA is still associated with ribosomes. Sequencing of mRNA degradation intermediates revealed that the complete deadenylation of the mRNA triggers its decapping and decay in both the 5′-3′ and the 3′-5′ directions. Contrary to the observations made for its mammalian homologs, overexpression of dTIS11 does not promote the localization of ARE-containing mRNAs in P-bodies but rather decreases the accumulation of CecA1 mRNA in these structures by enhancing the degradation process. Therefore, our results suggest that proteins of the TIS11 family may have acquired additional functions in the course of evolution from invertebrates to mammals.

scholarly journals Heat shock alters nuclear ribonucleoprotein assembly in Drosophila cells.

1983 ◽  
Vol 3 (2) ◽  
pp. 161-171 ◽  
Author(s):  
S Mayrand ◽  
T Pederson
Keyword(s):  
Heat Shock ◽  
Mammalian Cells ◽  
Cultured Cells ◽  
Particle Structure ◽  
Nuclear Maturation ◽  
Shock Response ◽  
Nuclear Rna ◽  
Nuclear Ribonucleoprotein ◽  
Drosophila Cells

Heterogeneous nuclear RNA is normally complexed with a specific set of proteins, forming ribonucleoprotein particles termed hnRNP. These particles are likely to be involved in mRNA processing. We have found that the structure of hnRNP is profoundly altered during the heat shock response in Drosophila cultured cells. Although hnRNA continues to be synthesized at a near-normal rate during heat shock, its assembly into hnRNP is incomplete, as evidenced by a greatly decreased protein content of the particles in Cs2SO4 density gradients. RNA-protein cross-linking conducted in vivo (Mayrand and Pederson, Proc. Natl. Acad. Sci. U.S.A. 78:2208-2212, 1981) also reveals that hnRNA made during heat shock is complexed with greatly reduced amounts of protein. The block of hnRNP assembly occurs immediately upon heat shock, even before the onset of heat shock protein synthesis. Additional experiments reveal that hnRNP assembled normally at 25 degrees C subsequently disassembles during heat shock. The capacity for normal hnRNP assembly is gradually restored after heat-shocked cells are returned to 25 degrees C. Heat-shocked mammalian cells also show a similar block in hnRNP assembly. We suggest that incomplete assembly of hnRNP during heat shock leads to abortive processing of most mRNA precursors and favors the processing or export (or both) of others whose pathway of nuclear maturation is less dependent on, or even independent of, normal hnRNP particle structure. This hypothesis is compatible with a large number of previous observations.

scholarly journals Biophysical Characterization and Computational Modeling of Histone mRNA Degradation Intermediates

2021 ◽  
Vol 35 (S1) ◽  
Author(s):  
Morgan Shine ◽  
Kendy Pellegrene ◽  
Mihaela Mihailescu ◽  
Jeffrey Evanseck ◽  
Patrick Lackey
Keyword(s):  
Computational Modeling ◽  
Mrna Degradation ◽  
Histone Mrna ◽  
Biophysical Characterization ◽  
Degradation Intermediates

scholarly journals Re-polyadenylation occurs predominantly on maternal mRNA degradation intermediates during mammalian oocyte-to-embryo transition

2021 ◽  
Author(s):  
Yusheng Liu ◽  
Yiwei Zhang ◽  
Hu Nie ◽  
Zhonghua Liu ◽  
Jiaqiang Wang ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Mrna Degradation ◽  
Mammalian Oocyte ◽  
Maternal Mrna ◽  
Early Embryos ◽  
Specific Regulation ◽  
And Function ◽  
Post Transcriptional Regulation ◽  
Degradation Intermediates ◽  
Polyadenylated Mrna

The nascent mRNA transcribed in the nucleus is cleaved and polyadenylated before it is transported to the cytoplasm for translation. Polyadenylation can also occur in the cytoplasm for post-transcriptional regulation, especially in neurons, oocytes and early embryos. Recently, we revealed transcriptome-wide maternal mRNA cytoplasmic re-polyadenylation during the mammalian oocyte-to-embryo transition (OET). However, the mechanism of re-polyadenylation during mammalian OET, including the sites to be re-polyadenylated and the enzymes involved, is still poorly understood. Here, by analyzing the PAIso-seq1 and PAIso-seq2 poly(A) inclusive transcriptome data during OET in mice, rats, pigs, and humans, we reveal conserved re-polyadenylation of mRNA degradation intermediates. These re-polyadenylated mRNA degradation intermediates account for over half of the polyadenylated mRNA during OET in all four species. We find that mRNA degradation intermediates for re-polyadenylation are generated through Btg4-mediated deadenylation in both mouse and human. Interestingly, the poly(A) tails on the re-polyadenylated mRNA degradation intermediates are of different lengths and contain different levels of non-A residues compared to regular polyadenylation sites, suggesting specific regulation and function of these poly(A) tails in mammalian OET. Together, our findings reveal the maternal mRNA degradation intermediates as substrates for conserved cytoplasmic dominant re-polyadenylation during mammalian OET, and uncover the mechanism of production of these mRNA degradation intermediates. These findings provide new insights into mRNA post-transcriptional regulation, and a new direction for the study of mammalian OET.

scholarly journals Following Temperature Stress, Export of Heat Shock mRNA Occurs Efficiently in Cells with Mutations in Genes Normally Important for mRNA Export

2007 ◽  
Vol 6 (3) ◽  
pp. 505-513 ◽  
Author(s):  
Christiane Rollenhagen ◽  
Christine A. Hodge ◽  
Charles N. Cole
Keyword(s):  
Heat Shock ◽  
Binding Proteins ◽  
Fluorescent Protein ◽  
Mrna Export ◽  
Temperature Sensitive ◽  
Mrna Binding Proteins ◽  
Tho Complex ◽  
Green Fluorescent ◽  
Mrna Binding

ABSTRACT Heat shock leads to accumulation of polyadenylated RNA in nuclei of Saccharomyces cerevisiae cells, transcriptional induction of heat shock genes, and efficient export of polyadenylated heat shock mRNAs. These studies were conducted to examine the requirements for export of mRNA following heat shock. We used in situ hybridization to detect SSA4 mRNA (encoding Hsp70) and flow cytometry to measure the amount of Ssa4p-green fluorescent protein (GFP) produced following heat shock. Npl3p and Yra1p are mRNA-binding proteins recruited to nascent mRNAs and are essential for proper mRNA biogenesis and export. Heat shock mRNA was exported efficiently in temperature-sensitive npl3, yra1, and npl3 yra1 mutant strains. Nevertheless, Yra1p was recruited to heat shock mRNA, as were Nab2p and Npl3p. Interestingly, Yra1p was not recruited to heat shock mRNA in yra1-1 cells, suggesting that Npl3p is required for recruitment of Yra1p. The THO complex, which functions in transcription elongation and in recruitment of Yra1p, was not required for heat shock mRNA export, although normal mRNA export is impaired in growing cells lacking THO complex proteins. Taken together, these studies indicate that export following heat shock depends upon fewer factors than does mRNA export in growing cells. Furthermore, even though some mRNA-binding proteins are dispensable for efficient export of heat shock mRNA, those that are present in nuclei of heat shocked cells were recruited to heat shock mRNA.

Changes in mRNA Degradation Efficiencies under Varying Conditions Are Regulated by Multiple Determinants in Arabidopsis thaliana

2020 ◽  
Author(s):  
Daishin Ueno ◽  
Maki Mikami ◽  
Shotaro Yamasaki ◽  
Miho Kaneko ◽  
Takafumi Mukuta ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Developmental Stages ◽  
Cultured Cells ◽  
Growth Conditions ◽  
Mrna Degradation ◽  
Translation Efficiency ◽  
Sequence Motifs ◽  
Mrna Accumulation ◽  
Mrna Length ◽  
Degradation Intermediates

Abstract Multiple mechanisms are involved in gene expression, with mRNA degradation being critical for the control of mRNA accumulation. In plants, although some trans-acting factors and motif sequences have been identified in deadenylation-dependent mRNA degradation, endonucleolytic cleavage-dependent mRNA degradation has not been studied in detail. Previously, we developed truncated RNA-end sequencing (TREseq) in Arabidopsis thaliana and detected G-rich sequence motifs around 5′ degradation intermediates. However, it remained to be elucidated whether degradation efficiencies of 5′ degradation intermediates in A. thaliana vary among growth conditions and developmental stages. To address this issue, we conducted TREseq of cultured cells under heat stress and at three developmental stages (seedlings, expanding leaves and expanded leaves) and compared 5′ degradation intermediates data among the samples. Although some 5′ degradation intermediates had almost identical degradation efficiencies, others differed among conditions. We focused on the genes and sites whose degradation efficiencies differed. Changes in degradation efficiencies at the gene and site levels revealed an effect on mRNA accumulation in all comparisons. These changes in degradation efficiencies involved multiple determinants, including mRNA length and translation efficiency. These results suggest that several determinants govern the efficiency of mRNA degradation in plants, helping the organism to adapt to varying conditions by controlling mRNA accumulation.

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