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Kumar K, Sinha SK, Maity U, Kirti PB, Kumar KRR. Insights into established and emerging roles of SR protein family in plants and animals. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1763. [PMID: 36131558 DOI: 10.1002/wrna.1763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 08/11/2022] [Accepted: 08/22/2022] [Indexed: 05/13/2023]
Abstract
Splicing of pre-mRNA is an essential part of eukaryotic gene expression. Serine-/arginine-rich (SR) proteins are highly conserved RNA-binding proteins present in all metazoans and plants. SR proteins are involved in constitutive and alternative splicing, thereby regulating the transcriptome and proteome diversity in the organism. In addition to their role in splicing, SR proteins are also involved in mRNA export, nonsense-mediated mRNA decay, mRNA stability, and translation. Due to their pivotal roles in mRNA metabolism, SR proteins play essential roles in normal growth and development. Hence, any misregulation of this set of proteins causes developmental defects in both plants and animals. SR proteins from the animal kingdom are extensively studied for their canonical and noncanonical functions. Compared with the animal kingdom, plant genomes harbor more SR protein-encoding genes and greater diversity of SR proteins, which are probably evolved for plant-specific functions. Evidence from both plants and animals confirms the essential role of SR proteins as regulators of gene expression influencing cellular processes, developmental stages, and disease conditions. This article is categorized under: RNA Processing > Splicing Mechanisms RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Kundan Kumar
- Department of Biotechnology, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
| | - Shubham Kumar Sinha
- Department of Biotechnology, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
| | - Upasana Maity
- Department of Biotechnology, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
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2
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Cyclophilins and Their Functions in Abiotic Stress and Plant-Microbe Interactions. Biomolecules 2021; 11:biom11091390. [PMID: 34572603 PMCID: PMC8464771 DOI: 10.3390/biom11091390] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/15/2021] [Accepted: 09/17/2021] [Indexed: 01/12/2023] Open
Abstract
Plants have developed a variety of mechanisms and regulatory pathways to change their gene expression profiles in response to abiotic stress conditions and plant–microbe interactions. The plant–microbe interaction can be pathogenic or beneficial. Stress conditions, both abiotic and pathogenic, negatively affect the growth, development, yield and quality of plants, which is very important for crops. In contrast, the plant–microbe interaction could be growth-promoting. One of the proteins involved in plant response to stress conditions and plant–microbe interactions is cyclophilin. Cyclophilins (CyPs), together with FK506-binding proteins (FKBPs) and parvulins, belong to a big family of proteins with peptidyl-prolyl cis-trans isomerase activity (Enzyme Commission (EC) number 5.2.1.8). Genes coding for proteins with the CyP domain are widely expressed in all organisms examined, including bacteria, fungi, animals, and plants. Their different forms can be found in the cytoplasm, endoplasmic reticulum, nucleus, chloroplast, mitochondrion and in the phloem space. They are involved in numerous processes, such as protein folding, cellular signaling, mRNA processing, protein degradation and apoptosis. In the past few years, many new functions, and molecular mechanisms for cyclophilins have been discovered. In this review, we aim to summarize recent advances in cyclophilin research to improve our understanding of their biological functions in plant defense and symbiotic plant–microbe interactions.
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3
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Park SY, Piao Y, Thomas C, Fuller GN, de Groot JF. Cdc2-like kinase 2 is a key regulator of the cell cycle via FOXO3a/p27 in glioblastoma. Oncotarget 2018; 7:26793-805. [PMID: 27050366 PMCID: PMC5042015 DOI: 10.18632/oncotarget.8471] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 03/10/2016] [Indexed: 01/09/2023] Open
Abstract
Cdc2-like kinase 2 (CLK2) is known as a regulator of RNA splicing that ultimately controls multiple physiological processes. However, the function of CLK2 in glioblastoma progression has not been described. Reverse-phase protein array (RPPA) was performed to identify proteins differentially expressed in CLK2 knockdown cells compared to controls. The RPPA results indicated that CLK2 knockdown influenced the expression of survival-, proliferation-, and cell cycle-related proteins in GSCs. Thus, knockdown of CLK2 expression arrested the cell cycle at the G1 and S checkpoints in multiple GSC lines. Depletion of CLK2 regulated the dephosphorylation of AKT and decreased phosphorylation of Forkhead box O3a (FOXO3a), which not only translocated to the nucleus but also increased p27 expression. In two glioblastoma xenograft models, the survival duration of mice with CLK2-knockdown GSCs was significantly longer than mice with control tumors. Additionally, tumor volumes were significantly smaller in CLK2-knockdown mice than in controls. Knockdown of CLK2 expression reduced the phosphorylation of FOXO3a and decreased Ki-67 in vivo. Finally, high expression of CLK2 protien was significantly associated with worse patient survival. These findings suggest that CLK2 plays a critical role in controlling the cell cycle and survival of glioblastoma via FOXO3a/p27.
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Affiliation(s)
- Soon Young Park
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yuji Piao
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Craig Thomas
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Gregory N Fuller
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - John F de Groot
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Pinto A, Malacrida B, Oieni J, Serafini MM, Davin A, Galbiati V, Corsini E, Racchi M. DHEA modulates the effect of cortisol on RACK1 expression via interference with the splicing of the glucocorticoid receptor. Br J Pharmacol 2015; 172:2918-27. [PMID: 25626076 PMCID: PMC4439885 DOI: 10.1111/bph.13097] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 12/21/2014] [Accepted: 01/21/2015] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND AND PURPOSE Dehydroepiandrosterone (DHEA) is thought to be an anti-glucocorticoid hormone known to be fully functional in young people but deficient in aged humans. Our previous data suggest that DHEA not only counteracts the effect of cortisol on RACK1 expression, a protein required both for the correct functioning of immune cells and for PKC-dependent pathway activation, but also modulates the inhibitory effect of cortisol on LPS-induced cytokine production. The purpose of this study was to investigate the effect of DHEA on the splicing mechanism of the human glucocorticoid receptor (GR). EXPERIMENTAL APPROACH The THP1 monocytic cell line was used as a cellular model. Cytokine production was measured by specific elisa. Western blot and real-time RT-PCR were used, where appropriate, to determine the effect of DHEA on GRs, serine/arginine-rich proteins (SRp), and RACK1 protein and mRNA. Small-interfering RNA was used to down-regulate GRβ. KEY RESULTS DHEA induced a dose-related up-regulation of GRβ and GRβ knockdown completely prevented DHEA-induced RACK1 expression and modulation of cytokine release. Moreover, we showed that DHEA influenced the expression of some components of the SRps found within the spliceosome, the main regulators of the alternative splicing of the GR gene. CONCLUSIONS AND IMPLICATIONS These data contribute to our understanding of the mechanism of action of DHEA and its effect on the immune system and as an anti-glucocorticoid agent.
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Affiliation(s)
- Antonella Pinto
- Department of Drug Sciences – Pharmacology, University of PaviaPavia, Italy
| | - Beatrice Malacrida
- Department of Drug Sciences – Pharmacology, University of PaviaPavia, Italy
| | - Jacopo Oieni
- Department of Drug Sciences – Pharmacology, University of PaviaPavia, Italy
| | | | | | - Valentina Galbiati
- Laboratory of Toxicology, DiSFeB, Università degli Studi di MilanoMilan, Italy
| | - Emanuela Corsini
- Laboratory of Toxicology, DiSFeB, Università degli Studi di MilanoMilan, Italy
| | - Marco Racchi
- Department of Drug Sciences – Pharmacology, University of PaviaPavia, Italy
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Hamperl S, Cimprich KA. The contribution of co-transcriptional RNA:DNA hybrid structures to DNA damage and genome instability. DNA Repair (Amst) 2014; 19:84-94. [PMID: 24746923 PMCID: PMC4051866 DOI: 10.1016/j.dnarep.2014.03.023] [Citation(s) in RCA: 185] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Accurate DNA replication and DNA repair are crucial for the maintenance of genome stability, and it is generally accepted that failure of these processes is a major source of DNA damage in cells. Intriguingly, recent evidence suggests that DNA damage is more likely to occur at genomic loci with high transcriptional activity. Furthermore, loss of certain RNA processing factors in eukaryotic cells is associated with increased formation of co-transcriptional RNA:DNA hybrid structures known as R-loops, resulting in double-strand breaks (DSBs) and DNA damage. However, the molecular mechanisms by which R-loop structures ultimately lead to DNA breaks and genome instability is not well understood. In this review, we summarize the current knowledge about the formation, recognition and processing of RNA:DNA hybrids, and discuss possible mechanisms by which these structures contribute to DNA damage and genome instability in the cell.
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Affiliation(s)
- Stephan Hamperl
- Department of Chemical, Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA
| | - Karlene A Cimprich
- Department of Chemical, Systems Biology, Stanford University School of Medicine, 318 Campus Drive, Stanford, CA 94305-5441, USA.
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Identification of a novel function of CX-4945 as a splicing regulator. PLoS One 2014; 9:e94978. [PMID: 24743259 PMCID: PMC3990583 DOI: 10.1371/journal.pone.0094978] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 03/21/2014] [Indexed: 12/25/2022] Open
Abstract
Alternative splicing is a nearly ubiquitous versatile process that controls gene expression and creates numerous protein isoforms with different functions from a single gene. The significance of alternative splicing has been confirmed by the increasing number of human diseases that are caused by misregulation of splicing events. Very few compounds, however, have been reported to act as inhibitors of alternative splicing, and their potential clinical use needs to be evaluated. Here, we report that CX-4945, a previously well-characterized inhibitor of casein kinase 2 (CK2) and a molecule currently in clinical trials (Phase II) for cancer treatment, regulates splicing in mammalian cells in a CK2-independent manner. Transcriptome-wide analysis using exon array also showed a widespread alteration in alternative splicing of numerous genes. We found that CX-4945 potently inhibits the Cdc2-like kinases (Clks) in vitro and in turn, leads to suppression of the phosphorylation of serine/arginine-rich (SR) proteins in mammalian cells. Surprisingly, the overall efficacy of CX-4945 on Clks (IC50 = 3-90 nM) was stronger than that of TG-003, the strongest inhibitor reported to date. Of the Clks, Clk2 was most strongly inhibited by CX-4945 in an ATP-competitive manner. Our research revealed an unexpected activity of the drug candidate CX-4945 as a potent splicing modulator and also suggested a potential application for therapy of diseases caused by abnormal splicing.
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Sen S, Jumaa H, Webster NJG. Splicing factor SRSF3 is crucial for hepatocyte differentiation and metabolic function. Nat Commun 2013; 4:1336. [PMID: 23299886 DOI: 10.1038/ncomms2342] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 11/28/2012] [Indexed: 12/23/2022] Open
Abstract
SR family RNA binding proteins regulate splicing of nascent RNAs in vitro but their physiological role in vivo is largely unexplored, as genetic deletion of many SR protein genes results in embryonic lethality. Here we show that SRSF3HKO mice carrying a hepatocyte-specific deletion of Srsf3 (homologous to human SRSF3/SRp20) have a disrupted hepatic architecture and show pre- and postnatal growth retardation. SRSF3HKO mice exhibit impaired hepatocyte maturation with alterations in glucose and lipid homeostasis characterized by reduced glycogen storage, fasting hypoglycemia, increased insulin sensitivity and reduced cholesterol synthesis. We identify various splicing alterations in the SRSF3HKO liver that explain the in vivo phenotype. In particular, loss of SRSF3 causes aberrant splicing of Hnf1α, Ern1, Hmgcs1, Dhcr7 and Scap genes, which are critical regulators of glucose and lipid metabolism. Our study provides the first evidence for a SRSF3-driven genetic programme required for morphological and functional differentiation of hepatocytes that may have relevance for human liver disease and metabolic dysregulation.
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Affiliation(s)
- Supriya Sen
- Medical Research Service, VA San Diego Healthcare System, 3350 La Jolla Village Drive, San Diego, California 92161, USA
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Zha X, Yan X, Shen Q, Zhang Y, Wu X, Chen S, Li B, Yang L, Geng S, Weng J, Du X, Li Y. Alternative expression of TCRζ related genes in patients with chronic myeloid leukemia. J Hematol Oncol 2012; 5:74. [PMID: 23228155 PMCID: PMC3544630 DOI: 10.1186/1756-8722-5-74] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 12/04/2012] [Indexed: 01/01/2023] Open
Abstract
A previous study has demonstrated a significant decrease in the TCRζ gene expression level in chronic myeloid leukemia (CML); thus, we further investigated the expression of TCRζ-regulating factors, the distribution of the TCRζ 3' untranslated region (3'-UTR) splice variants, and the expression level and correlation of the alternative splicing factor/splicing factor 2 (ASF/SF-2), FcεRIγ and ZAP-70 genes. TCRζ 3'-UTR splice variants were identified in peripheral blood mononuclear cells (PBMCs) from 14 healthy individuals, 40 patients with CML and 22 patients with CML in complete remission (CML-CR) by RT-PCR. The expression level of the TCRζ, FcεRIγ, ASF/SF-2 and ZAP-70 genes was analyzed by real-time quantitative PCR. While the expression of TCRζ gene in the CML group was significantly lower than that in the healthy individual and CML-CR groups, a significantly higher expression of the FceRIγ and ASF/SF-2 genes was found in the CML group. Two types of splicing forms were detected in all of the healthy individual CML-CR cases: wild type (WT) TCRζ 3'-UTR and alternatively splieced (AS) TCRζ 3'-UTR which have been alternatively splieced in the WT TCRζ 3'-UTR . However, 35% of the CML cases contained only the wild type TCRζ 3'-UTR isoform. Based on the TCRζ 3'-UTR isoform expression characteristic, we divided the patients with CML into two subgroups: the WT+AS- CML group, containing patients that express only the wild type TCRζ 3'-UTR, and the WT+AS+ CML group, which contained patients that expressed two TCRζ 3'-UTR isoforms. A significantly different ASF/SF-2 and FcεRIγ gene expression pattern was found between the WT+AS- and WT+AS+CML groups. We concluded that defective TCRζ expression may be characterized in the WT+AS-and WT+AS+CML subgroups by the different gene expression pattern. The overexpression of ASF/SF2, which alternatively splices the TCRζ 3'-UTR, is thought to participate in feedback regulation. The characteristics of TCRζ 3'-UTR alternative splicing may be a novel immunological marker for the evaluation of the CML immune status.
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Affiliation(s)
- Xianfeng Zha
- Institute of Hematology, Medical College, Jinan University, Guangzhou, 510632, China
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HMGA1a trapping of U1 snRNP at an authentic 5' splice site induces aberrant exon skipping in sporadic Alzheimer's disease. Mol Cell Biol 2010; 30:2220-8. [PMID: 20194618 DOI: 10.1128/mcb.00114-10] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Overexpression of high-mobility group A protein 1a (HMGA1a) causes aberrant exon 5 skipping of the Presenilin-2 (PS2) pre-mRNA, which is almost exclusively detected in patients with sporadic Alzheimer's disease. An electrophoretic mobility shift assay confirmed aberrant U1 small nuclear ribonucleoprotein particle (snRNP)-HMGA1a complex formation (via the U1-70K component), with RNA containing a specific HMGA1a-binding site and an adjacent 5' splice site. Psoralen cross-linking analysis demonstrated that the binding of HMGA1a adjacent to the 5' splice site induces unusually extended association of U1 snRNP to the 5' splice site. As a result, spliceosome assembly across either the intron or the exon is arrested at an early ATP-independent stage. We conclude that the HMGA1a-induced aberrant exon skipping is caused by impaired dissociation of U1 snRNP from the 5' splice site, leading to a defect in exon definition. The proposed molecular mechanism has profound implications for other known posttranscriptional modulation strategies in various organisms, all of which are triggered by aberrant U1 snRNP binding.
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10
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Schneider M, Hsiao HH, Will CL, Giet R, Urlaub H, Lührmann R. Human PRP4 kinase is required for stable tri-snRNP association during spliceosomal B complex formation. Nat Struct Mol Biol 2010; 17:216-21. [PMID: 20118938 DOI: 10.1038/nsmb.1718] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Accepted: 10/09/2009] [Indexed: 11/09/2022]
Abstract
Reversible protein phosphorylation has an essential role during pre-mRNA splicing. Here we identify two previously unidentified phosphoproteins in the human spliceosomal B complex, namely the pre-mRNA processing factors PRP6 and PRP31, both components of the U4/U6-U5 tri-small nuclear ribonucleoprotein (snRNP). We provide evidence that PRP6 and PRP31 are directly phosphorylated by human PRP4 kinase (PRP4K) concomitant with their incorporation into B complexes. Immunodepletion and complementation studies with HeLa splicing extracts revealed that active human PRP4K is required for the phosphorylation of PRP6 and PRP31 and for the assembly of stable, functional B complexes. Thus, the phosphorylation of PRP6 and PRP31 is likely to have a key role during spliceosome assembly. Our data provide new insights into the molecular mechanism by which PRP4K contributes to splicing. They further indicate that numerous phosphorylation events contribute to spliceosome assembly and, thus, that splicing can potentially be modulated at multiple regulatory checkpoints.
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Affiliation(s)
- Marc Schneider
- Department of Cellular Biochemistry, Max Planck Institute of Biophysical Chemistry, Göttingen, Germany
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11
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Tsianou D, Nikolakaki E, Tzitzira A, Bonanou S, Giannakouros T, Georgatsou E. The enzymatic activity of SR protein kinases 1 and 1a is negatively affected by interaction with scaffold attachment factors B1 and 2. FEBS J 2009; 276:5212-27. [PMID: 19674106 DOI: 10.1111/j.1742-4658.2009.07217.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
SR protein kinases (SRPKs) phosphorylate Ser/Arg dipeptide-containing proteins that play crucial roles in a broad spectrum of basic cellular processes. Phosphorylation by SRPKs constitutes a major way of regulating such cellular mechanisms. In the past, we have shown that SRPK1a interacts with the nuclear matrix protein scaffold attachment factor B1 (SAFB1) via its unique N-terminal domain, which differentiates it from SRPK1. In this study, we show that SAFB1 inhibits the activity of both SRPK1a and SRPK1 in vitro and that its RE-rich region is redundant for the observed inhibition. We demonstrate that kinase activity inhibition is caused by direct binding of SAFB1 to SRPK1a and SRPK1, and we also present evidence for the in vitro binding of SAFB2 to the two kinases, albeit with different affinity. Moreover, we show that both SR protein kinases can form complexes with both scaffold attachment factors B in living cells and that this interaction is capable of inhibiting their activity, depending on the tenacity of the complex formed. Finally, we present data demonstrating that SRPK/SAFB complexes are present in the nucleus of HeLa cells and that the enzymatic activity of the nuclear matrixlocalized SRPK1 is repressed. These results suggest a new role for SAFB proteins as regulators of SRPK activity and underline the importance of the assembly of transient intranuclear complexes in cellular regulation.
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Affiliation(s)
- Dora Tsianou
- Department of Medicine, University of Thessaly, Mezourlo, 41110 Larissa, Greece
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12
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Ricci EP, Mure F, Gruffat H, Decimo D, Medina-Palazon C, Ohlmann T, Manet E. Translation of intronless RNAs is strongly stimulated by the Epstein-Barr virus mRNA export factor EB2. Nucleic Acids Res 2009; 37:4932-43. [PMID: 19528074 PMCID: PMC2731895 DOI: 10.1093/nar/gkp497] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The Epstein–Barr virus protein (EB2) allows the nuclear export of a particular subset of early and late viral RNAs derived from intronless genes. EB2 is conserved among most herpesvirus members and its presence is essential for the production of infectious particles. Here we show that, besides its role as a nuclear export factor, EB2 strongly stimulates translation of unspliced mRNAs without affecting overall cellular translation. Interestingly, this effect can be reversed by the addition of an intron within the gene. The spliced mRNA is then efficiently exported and translated even in the absence of EB2. Moreover, we show that EB2 associates with translating ribosomes and increases the proportion of its target RNA in the polyribosomal fraction. Finally, testing of EB2 homolog proteins derived from EBV-related herpesviruses, shows that, even if they play similar roles within the replication cycle of their respective virus, their mechanisms of action are different.
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Affiliation(s)
- Emiliano P Ricci
- INSERM U758, Unité de Virologie Humaine, Ecole Normale Supérieure de Lyon, Lyon F-69007, France
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13
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Tanabe N, Kimura A, Yoshimura K, Shigeoka S. Plant-specific SR-related protein atSR45a interacts with spliceosomal proteins in plant nucleus. PLANT MOLECULAR BIOLOGY 2009; 70:241-52. [PMID: 19238562 DOI: 10.1007/s11103-009-9469-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Accepted: 02/08/2009] [Indexed: 05/08/2023]
Abstract
Serine/arginine-rich (SR) protein and its homologues (SR-related proteins) are important regulators of constitutive and/or alternative splicing and other aspects of mRNA metabolism. To clarify the contribution of a plant-specific and stress-responsive SR-related protein, atSR45a, to splicing events, here we analyzed the interaction of atSR45a with the other splicing factors by conducting a yeast two-hybrid assay and a bimolecular fluorescence complementation analysis. The atSR45a-1a and -2 proteins, the presumed mature forms produced by alternative splicing of atSR45a, interacted with U1-70K and U2AF(35)b, splicing factors for the initial definition of 5' and 3' splice sites, respectively, in the early stage of spliceosome assembly. Both proteins also interacted with themselves, other SR proteins (atSR45 and atSCL28), and PRP38-like protein, a homologue of the splicing factor essential for cleavage of the 5' splice site. The mapping of deletion mutants of atSR45a proteins revealed that the C-terminal arginine/serine-rich (RS) domain of atSR45a proteins are required for the interaction with U1-70K, U2AF(35)b, atSR45, atSCL28, PRP38-like protein, and themselves, and the N-terminal RS domain enhances the interaction efficiency. Interestingly, the distinctive N-terminal extension in atSR45a-1a protein, but not atSR45a-2 protein, inhibited the interaction with these splicing factors. These findings suggest that the atSR45a proteins help to form the bridge between 5' and 3' splice sites in the spliceosome assembly and the efficiency of spliceosome formation is affected by the expression ratio of atSR45a-1a and atSR45a-2.
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Affiliation(s)
- Noriaki Tanabe
- Department of Advanced Bioscience, Faculty of Agriculture, Kinki University, Nakamachi, Nara, Japan
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14
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Björk P, Jin S, Zhao J, Singh OP, Persson JO, Hellman U, Wieslander L. Specific combinations of SR proteins associate with single pre-messenger RNAs in vivo and contribute different functions. J Cell Biol 2009; 184:555-68. [PMID: 19221196 PMCID: PMC2654125 DOI: 10.1083/jcb.200806156] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2008] [Accepted: 01/14/2009] [Indexed: 02/03/2023] Open
Abstract
Serine/arginine-rich (SR) proteins are required for messenger RNA (mRNA) processing, export, surveillance, and translation. We show that in Chironomus tentans, nascent transcripts associate with multiple types of SR proteins in specific combinations. Alternative splicing factor (ASF)/SF2, SC35, 9G8, and hrp45/SRp55 are all present in Balbiani ring (BR) pre-messenger ribonucleoproteins (mRNPs) preferentially when introns appear in the pre-mRNA and when cotranscriptional splicing takes place. However, hrp45/SRp55 is distributed differently in the pre-mRNPs along the gene compared with ASF/SF2, SC35, and 9G8, suggesting functional differences. All four SR proteins are associated with the BR mRNPs during export to the cytoplasm. Interference with SC35 indicates that SC35 is important for the coordination of splicing, transcription, and 3' end processing and also for nucleocytoplasmic export. ASF/SF2 is associated with polyribosomes, whereas SC35, 9G8, and hrp45/SRp55 cosediment with monoribosomes. Thus, individual endogenous pre-mRNPs/mRNPs bind multiple types of SR proteins during transcription, and these SR proteins accompany the mRNA and play different roles during the gene expression pathway in vivo.
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Affiliation(s)
- Petra Björk
- Department of Molecular Biology and Functional Genomics and Department of Mathematics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - ShaoBo Jin
- Department of Molecular Biology and Functional Genomics and Department of Mathematics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Jian Zhao
- Department of Molecular Biology and Functional Genomics and Department of Mathematics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Om Prakash Singh
- Department of Molecular Biology and Functional Genomics and Department of Mathematics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Jan-Olov Persson
- Department of Molecular Biology and Functional Genomics and Department of Mathematics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Ulf Hellman
- Ludwig Institute for Cancer Research, SE-751 24 Uppsala, Sweden
| | - Lars Wieslander
- Department of Molecular Biology and Functional Genomics and Department of Mathematics, Stockholm University, SE-106 91 Stockholm, Sweden
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15
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Mechanisms employed by retroviruses to exploit host factors for translational control of a complicated proteome. Retrovirology 2009; 6:8. [PMID: 19166625 PMCID: PMC2657110 DOI: 10.1186/1742-4690-6-8] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2008] [Accepted: 01/24/2009] [Indexed: 12/14/2022] Open
Abstract
Retroviruses have evolved multiple strategies to direct the synthesis of a complex proteome from a single primary transcript. Their mechanisms are modulated by a breadth of virus-host interactions, which are of significant fundamental interest because they ultimately affect the efficiency of virus replication and disease pathogenesis. Motifs located within the untranslated region (UTR) of the retroviral RNA have established roles in transcriptional trans-activation, RNA packaging, and genome reverse transcription; and a growing literature has revealed a necessary role of the UTR in modulating the efficiency of viral protein synthesis. Examples include a 5' UTR post-transcriptional control element (PCE), present in at least eight retroviruses, that interacts with cellular RNA helicase A to facilitate cap-dependent polyribosome association; and 3' UTR constitutive transport element (CTE) of Mason-Pfizer monkey virus that interacts with Tap/NXF1 and SR protein 9G8 to facilitate RNA export and translational utilization. By contrast, nuclear protein hnRNP E1 negatively modulates HIV-1 Gag, Env, and Rev protein synthesis. Alternative initiation strategies by ribosomal frameshifting and leaky scanning enable polycistronic translation of the cap-dependent viral transcript. Other studies posit cap-independent translation initiation by internal ribosome entry at structural features of the 5' UTR of selected retroviruses. The retroviral armamentarium also commands mechanisms to counter cellular post-transcriptional innate defenses, including protein kinase R, 2',5'-oligoadenylate synthetase and the small RNA pathway. This review will discuss recent and historically-recognized insights into retrovirus translational control. The expanding knowledge of retroviral post-transcriptional control is vital to understanding the biology of the retroviral proteome. In a broad perspective, each new insight offers a prospective target for antiviral therapy and strategic improvement of gene transfer vectors.
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16
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Kim DJ, Oh B, Kim YY. Splicing factor ASF/SF2 and transcription factor PPAR-gamma cooperate to directly regulate transcription of uncoupling protein-3. Biochem Biophys Res Commun 2008; 378:877-82. [PMID: 19073146 DOI: 10.1016/j.bbrc.2008.12.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2008] [Accepted: 12/03/2008] [Indexed: 11/30/2022]
Abstract
The different isoforms of the uncoupling protein-3 (UCP3) are expressed in skeletal muscle and are up-regulated by splicing factors. Here, we report that UCP3 alternative splicing (alternative polyadenylation) is regulated by cooperation between the splicing factor ASF/SF2 and the transcription factor PPAR-gamma. We found that ASF/SF2 activates formation of long-form UCP3 (UCP3(L)) by inhibiting a cleavage and polyadenylation signal (AATAAA) located in its final intron that prematurely terminates message elongation. PPAR-gamma activates this process by directly interacting with ASF/SF2, providing the first example of a direct link between a transcription factor and alternative splicing. Activation of ASF/SF2 promotes formation of UCP3(L), whereas loss of ASF/SF2 decreases production of both UCP3(L) and short-form UCP3 (UCP3(S)). We suggest that the relative abundance of ASF/SF2 and PPAR-gamma determines the ratio of UCP3 isoforms.
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Affiliation(s)
- Dong-Joon Kim
- Center for Genome Science, National Institute of Health in Korea, Eunpyung-Gu, Seoul, Republic of Korea
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17
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Merdzhanova G, Edmond V, De Seranno S, Van den Broeck A, Corcos L, Brambilla C, Brambilla E, Gazzeri S, Eymin B. E2F1 controls alternative splicing pattern of genes involved in apoptosis through upregulation of the splicing factor SC35. Cell Death Differ 2008; 15:1815-23. [DOI: 10.1038/cdd.2008.135] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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18
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Abstract
The general organization ofeukaryotic nuclei, including plant nuclei, into functional domains is now widely recognized. Conventional immunocytochemistry and visualization of proteins fused to fluorescent proteins (FP) have revealed that in plants, RNA and protein components of pre-mRNA splicing are spatially organized depending on the stage of cell cycle, development, and the cell's physiological state. Application of some of the latest microscopy techniques, which reveal biophysical properties such as diffusion and interaction properties of proteins, has begun to provide important insights into the functional organization of spliceosomal proteins in plants. Although some progress has been made in understanding the spatial and temporal organization of splicing machinery in plants, the mechanisms that regulate this organization and its functional consequences remain unresolved.
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19
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Abstract
A substantial fraction (approximately 30%) of plant genes is alternatively spliced, but how alternative splicing is regulated remains unknown. Many plant genes undergo alternative splicing in response to a variety of stresses. Large-scale computational analyses and experimental approaches focused on select genes are beginning to reveal that alternative splicing constitutes an integral part of gene regulation in stress responses. Based on the studies discussed in this chapter, it appears that alternative splicing generates transcriptome/proteome complexity that is likely to be important for stress adaptation. However, the signaling pathways that relay stress conditions to splicing machinery and if and how the alternative spliced products confer adaptive advantages to plants are poorly understood.
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20
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Cloutier P, Toutant J, Shkreta L, Goekjian S, Revil T, Chabot B. Antagonistic Effects of the SRp30c Protein and Cryptic 5 ′ Splice Sites on the Alternative Splicing of the Apoptotic Regulator Bcl-x. J Biol Chem 2008; 283:21315-24. [DOI: 10.1074/jbc.m800353200] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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21
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Hai Y, Cao W, Liu G, Hong SP, Elela SA, Klinck R, Chu J, Xie J. A G-tract element in apoptotic agents-induced alternative splicing. Nucleic Acids Res 2008; 36:3320-31. [PMID: 18440980 PMCID: PMC2425498 DOI: 10.1093/nar/gkn207] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Alternative splicing of a single pre-mRNA transcript can produce protein isoforms that promote either cell growth or death. Here we show that Ro-31-8220 (Ro), an apoptotic agent that inhibits protein kinase C and activates the c-Jun N terminal kinase, decreased the proportion of the cell growth-promoting Bcl-xL splice variant. Targeted mutagenesis analyses narrowed down a critical sequence to a 16-nt G-tract element (Gt16). Transferring this element to a heterologous gene conferred Ro response on an otherwise constitutive exon. The Ro effect was reduced by okadaic acid, an inhibitor of protein phosphatases PP1 and PP2A, in a concentration-dependent manner. Search in the human genome followed by RT–PCR identified a group of genes that contain similar exonic G-tract elements and are responsive to Ro. Moreover, the Gt16 element also mediates the regulation of alternative splicing by other cell apoptosis-inducers particularly retinoic acid. Therefore, the G-tract element likely plays a role in the apoptotic agents-induced alternative splicing of a group of genes. The functions of these genes imply that this regulation will have impact on cell growth/death.
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Affiliation(s)
- Yan Hai
- Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College. Kunming, China
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22
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Bakkour N, Lin YL, Maire S, Ayadi L, Mahuteau-Betzer F, Nguyen CH, Mettling C, Portales P, Grierson D, Chabot B, Jeanteur P, Branlant C, Corbeau P, Tazi J. Small-molecule inhibition of HIV pre-mRNA splicing as a novel antiretroviral therapy to overcome drug resistance. PLoS Pathog 2008; 3:1530-9. [PMID: 17967062 PMCID: PMC2042022 DOI: 10.1371/journal.ppat.0030159] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2007] [Accepted: 09/14/2007] [Indexed: 01/01/2023] Open
Abstract
The development of multidrug-resistant viruses compromises antiretroviral therapy efficacy and limits therapeutic options. Therefore, it is an ongoing task to identify new targets for antiretroviral therapy and to develop new drugs. Here, we show that an indole derivative (IDC16) that interferes with exonic splicing enhancer activity of the SR protein splicing factor SF2/ASF suppresses the production of key viral proteins, thereby compromising subsequent synthesis of full-length HIV-1 pre-mRNA and assembly of infectious particles. IDC16 inhibits replication of macrophage- and T cell-tropic laboratory strains, clinical isolates, and strains with high-level resistance to inhibitors of viral protease and reverse transcriptase. Importantly, drug treatment of primary blood cells did not alter splicing profiles of endogenous genes involved in cell cycle transition and apoptosis. Thus, human splicing factors represent novel and promising drug targets for the development of antiretroviral therapies, particularly for the inhibition of multidrug-resistant viruses.
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Affiliation(s)
- Nadia Bakkour
- Université de Montpellier II, Montpellier, France
- Institut de Génétique Moléculaire de Montpellier, Montpellier, France
- CNRS, UMR 5535, Montpellier, France
| | - Yea-Lih Lin
- Laboratoire d'Immunologie CHU de Montpellier, Montpellier, France
- Institut de Genetique Humaine, Montpellier, France
- CNRS, UPR1142, Montpellier, France
| | - Sophie Maire
- Université de Montpellier II, Montpellier, France
- Institut de Génétique Moléculaire de Montpellier, Montpellier, France
- CNRS, UMR 5535, Montpellier, France
| | - Lilia Ayadi
- Université Henri Poincare-Nancy I, Vandoeuvre-les-Nancy, France
- CNRS, UMR 7567, Vandoeuvre-les-Nancy, France
| | | | - Chi Hung Nguyen
- Laboratoire de Pharmaco-chimie, Institut Curie, Orsay, France
- CNRS-UMR 176, Orsay, France
| | - Clément Mettling
- Laboratoire d'Immunologie CHU de Montpellier, Montpellier, France
- Institut de Genetique Humaine, Montpellier, France
- CNRS, UPR1142, Montpellier, France
| | - Pierre Portales
- Laboratoire d'Immunologie CHU de Montpellier, Montpellier, France
- Institut de Genetique Humaine, Montpellier, France
- CNRS, UPR1142, Montpellier, France
| | - David Grierson
- Laboratoire de Pharmaco-chimie, Institut Curie, Orsay, France
- CNRS-UMR 176, Orsay, France
| | - Benoit Chabot
- Département de Microbiologie et d'Infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Philippe Jeanteur
- Université de Montpellier II, Montpellier, France
- Institut de Génétique Moléculaire de Montpellier, Montpellier, France
- CNRS, UMR 5535, Montpellier, France
| | - Christiane Branlant
- Université Henri Poincare-Nancy I, Vandoeuvre-les-Nancy, France
- CNRS, UMR 7567, Vandoeuvre-les-Nancy, France
| | - Pierre Corbeau
- Laboratoire d'Immunologie CHU de Montpellier, Montpellier, France
- Institut de Genetique Humaine, Montpellier, France
- CNRS, UPR1142, Montpellier, France
| | - Jamal Tazi
- Université de Montpellier II, Montpellier, France
- Institut de Génétique Moléculaire de Montpellier, Montpellier, France
- CNRS, UMR 5535, Montpellier, France
- * To whom correspondence should be addressed. E-mail:
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23
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Kpebe A, Rabinow L. Alternative promoter usage generates multiple evolutionarily conserved isoforms ofDrosophila DOA kinase. Genesis 2008; 46:132-43. [DOI: 10.1002/dvg.20374] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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24
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Revil T, Toutant J, Shkreta L, Garneau D, Cloutier P, Chabot B. Protein kinase C-dependent control of Bcl-x alternative splicing. Mol Cell Biol 2007; 27:8431-41. [PMID: 17923691 PMCID: PMC2169420 DOI: 10.1128/mcb.00565-07] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2007] [Revised: 05/07/2007] [Accepted: 09/19/2007] [Indexed: 02/07/2023] Open
Abstract
The alternative splicing of Bcl-x generates the proapoptotic Bcl-x(S) protein and the antiapoptotic isoform Bcl-x(L). Bcl-x splicing is coupled to signal transduction, since ceramide, hormones, and growth factors alter the ratio of the Bcl-x isoforms in different cell lines. Here we report that the protein kinase C (PKC) inhibitor and apoptotic inducer staurosporine switches the production of Bcl-x towards the x(S) mRNA isoform in 293 cells. The increase in Bcl-x(S) elicited by staurosporine likely involves signaling events that affect splicing decisions, because it requires active transcription and no new protein synthesis and is independent of caspase activation. Moreover, the increase in Bcl-x(S) is reproduced with more specific inhibitors of PKC. Alternative splicing of the receptor tyrosine kinase gene Axl is similarly affected by staurosporine in 293 cells. In contrast to the case for 293 cells, PKC inhibitors do not influence the alternative splicing of Bcl-x and Axl in cancer cell lines, suggesting that these cells have sustained alterations that uncouple splicing decisions from PKC-dependent signaling. Using minigenes, we show that an exonic region located upstream of the Bcl-x(S) 5' splice site is important to mediate the staurosporine shift in Bcl-x splicing. When transplanted to other alternative splicing units, portions of this region confer splicing modulation and responsiveness to staurosporine, suggesting the existence of factors that couple splicing decisions with PKC signaling.
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Affiliation(s)
- Timothée Revil
- RNA/RNP Group, Département de Microbiologie et d'Infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4
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25
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Abstract
Alternative pre-mRNA splicing has an important role in the control of neuronal gene expression. Many neuronal proteins are structurally diversified through the differential inclusion and exclusion of sequences in the final spliced mRNA. Here, we discuss common mechanisms of splicing regulation and provide examples of how alternative splicing has important roles in neuronal development and mature neuron function. Finally, we describe regulatory proteins that control the splicing of some neuronally expressed transcripts.
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Affiliation(s)
- Qin Li
- Howard Hughes Medical Institute, University of California, Los Angeles, 6-762 MacDonald Research Laboratories, 675 Charles E. Young Drive South, Los Angeles, California 90095, USA
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26
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Zhu J, Gong JY, Goodman OB, Cartegni L, Nanus DM, Shen R. Bombesin attenuates pre-mRNA splicing of glucocorticoid receptor by regulating the expression of serine-arginine protein p30c (SRp30c) in prostate cancer cells. BIOCHIMICA ET BIOPHYSICA ACTA 2007; 1773:1087-94. [PMID: 17540466 PMCID: PMC1939980 DOI: 10.1016/j.bbamcr.2007.04.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2007] [Revised: 04/17/2007] [Accepted: 04/20/2007] [Indexed: 11/19/2022]
Abstract
Although glucocorticoids are frequently administered to patients with hormone refractory prostate cancer, their therapeutic effectiveness is limited by the development of glucocorticoid resistance. The molecular mechanisms of glucocorticoid resistance are unknown but are believed to involve neuropeptide growth factors and cytokines. We examined the functional interaction between bombesin and dexamethasone in PC-3 cells and found that bombesin could act as a survival factor by interfering with dexamethasone-mediated growth inhibition. Because glucocorticoids exert their effects through glucocorticoid receptors (GRs), we measured the expression of GR alpha and GR beta isoforms in the presence of bombesin. Western blotting and real time PCR revealed bombesin induced expression of GR beta, but not GR alpha. Because GR isoforms are generated by alternative splicing of a common GR gene, we examined the expression of serine-arginine (SR) proteins involved in alternative splicing, and found that the expression of SRp30 was induced by bombesin in PC-3 cells. To characterize the role of SRp30 in splicing of GR isoforms, siRNAs specific to various SRp30 isoforms were transfected into PC-3 cells. We found that suppression of SRp30c expression by siRNA specifically antagonized bombesin's effect on glucocorticoid-mediated inhibition of PC cells, suggesting that bombesin-induced expression of SRp30c affects GR pre-mRNA splicing, leading to increased GR beta expression and contributing to glucocorticoid resistance in PC cells.
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Affiliation(s)
- Jin Zhu
- Department of Urology, Weill Medical College of Cornell University and New York Presbyterian Hospital, New York, NY
| | - Jun Y. Gong
- Department of Urology, Weill Medical College of Cornell University and New York Presbyterian Hospital, New York, NY
| | - Oscar B. Goodman
- Department of Medicine, Weill Medical College of Cornell University and New York Presbyterian Hospital, New York, NY
| | - Luca Cartegni
- Department of Molecular Pharmacology and Chemistry, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David M. Nanus
- Department of Urology, Weill Medical College of Cornell University and New York Presbyterian Hospital, New York, NY
- Department of Medicine, Weill Medical College of Cornell University and New York Presbyterian Hospital, New York, NY
| | - Ruoqian Shen
- Department of Urology, Weill Medical College of Cornell University and New York Presbyterian Hospital, New York, NY
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27
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Ali GS, Palusa SG, Golovkin M, Prasad J, Manley JL, Reddy AS. Regulation of plant developmental processes by a novel splicing factor. PLoS One 2007; 2:e471. [PMID: 17534421 PMCID: PMC1868597 DOI: 10.1371/journal.pone.0000471] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2007] [Accepted: 04/28/2007] [Indexed: 11/18/2022] Open
Abstract
Serine/arginine-rich (SR) proteins play important roles in constitutive and alternative splicing and other aspects of mRNA metabolism. We have previously isolated a unique plant SR protein (SR45) with atypical domain organization. However, the biological and molecular functions of this novel SR protein are not known. Here, we report biological and molecular functions of this protein. Using an in vitro splicing complementation assay, we showed that SR45 functions as an essential splicing factor. Furthermore, the alternative splicing pattern of transcripts of several other SR genes was altered in a mutant, sr45-1, suggesting that the observed phenotypic abnormalities in sr45-1 are likely due to altered levels of SR protein isoforms, which in turn modulate splicing of other pre-mRNAs. sr45-1 exhibited developmental abnormalities, including delayed flowering, narrow leaves and altered number of petals and stamens. The late flowering phenotype was observed under both long days and short days and was rescued by vernalization. FLC, a key flowering repressor, is up-regulated in sr45-1 demonstrating that SR45 influences the autonomous flowering pathway. Changes in the alternative splicing of SR genes and the phenotypic defects in the mutant were rescued by SR45 cDNA, further confirming that the observed defects in the mutant are due to the lack of SR45. These results indicate that SR45 is a novel plant-specific splicing factor that plays a crucial role in regulating developmental processes.
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Affiliation(s)
- Gul Shad Ali
- Department of Biology and Program in Molecular Plant Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Saiprasad G. Palusa
- Department of Biology and Program in Molecular Plant Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Maxim Golovkin
- Department of Biology and Program in Molecular Plant Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Jayendra Prasad
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - James L. Manley
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Anireddy S.N. Reddy
- Department of Biology and Program in Molecular Plant Biology, Colorado State University, Fort Collins, Colorado, United States of America
- * To whom correspondence should be addressed. E-mail:
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28
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Lukasiewicz R, Velazquez-Dones A, Huynh N, Hagopian J, Fu XD, Adams J, Ghosh G. Structurally unique yeast and mammalian serine-arginine protein kinases catalyze evolutionarily conserved phosphorylation reactions. J Biol Chem 2007; 282:23036-43. [PMID: 17517895 DOI: 10.1074/jbc.m611305200] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mammalian serine-arginine (SR) protein, ASF/SF2, contains multiple contiguous RS dipeptides at the C terminus, and approximately 12 of these serines are processively phosphorylated by the SR protein kinase 1 (SRPK1). We have recently shown that a docking motif in ASF/SF2 specifically interacts with a groove in SRPK1, and this interaction is necessary for processive phosphorylation. We previously showed that SRPK1 and its yeast ortholog Sky1p maintain their active conformations using diverse structural strategies. Here we tested if the mechanism of ASF/SF2 phosphorylation by SRPK is evolutionarily conserved. We show that Sky1p forms a stable complex with its heterologous mammalian substrate ASF/SF2 and processively phosphorylates the same sites as SRPK1. We further show that Sky1p utilizes the same docking groove to bind yeast SR-like protein Gbp2p and phosphorylates all three serines present in a contiguous RS dipeptide stretch. However, the mechanism of Gbp2p phosphorylation appears to be non-processive. Thus, there are physical attributes of SR and SR-like substrates that dictate the mechanism of phosphorylation, whereas the ability to processively phosphorylate substrates is inherent to SR protein kinases.
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Affiliation(s)
- Randall Lukasiewicz
- Department of Chemistry & Biochemistry, University of California, San Diego, La Jolla, California 92093-0375, USA
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29
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Swartz JE, Bor YC, Misawa Y, Rekosh D, Hammarskjold ML. The shuttling SR protein 9G8 plays a role in translation of unspliced mRNA containing a constitutive transport element. J Biol Chem 2007; 282:19844-53. [PMID: 17513303 DOI: 10.1074/jbc.m701660200] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The splicing regulatory SR protein, 9G8, has recently been proposed to function in mRNA export in conjunction with the export protein, Tap/NXF1. Tap interacts directly with the Mason-Pfizer monkey virus constitutive transport element (CTE), an element that enables export of unspliced, intron-containing mRNA. Based on our previous finding that Tap can promote polysome association and translation of CTE-RNA, we investigated the effect of 9G8 on cytoplasmic RNA fate. 9G8 was shown to enhance expression of unspliced RNA containing either the Mason-Pfizer monkey virus-CTE or the recently discovered Tap-CTE. 9G8 also enhanced polyribosome association of unspliced RNA containing a CTE. Hyperphosphorylated 9G8 was present in monosomes and small polyribosomes, whereas soluble fractions contained only hypophosphorylated protein. Our results are consistent with a model in which hypophosphorylated SR proteins remain stably associated with messenger ribonucleoprotein (mRNP) complexes during export and are released during translation initiation concomitant with increased phosphorylation. These results provide further evidence for crucial links between RNA splicing, export and translation.
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Affiliation(s)
- Jennifer E Swartz
- Myles H. Thaler Center for AIDS and Human Retrovirus Research and Department of Microbiology, University of Virginia, Charlottesville, Virginia 22908, USA
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30
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Gullerova M, Barta A, Lorkovic ZJ. Rct1, a nuclear RNA recognition motif-containing cyclophilin, regulates phosphorylation of the RNA polymerase II C-terminal domain. Mol Cell Biol 2007; 27:3601-11. [PMID: 17339332 PMCID: PMC1900001 DOI: 10.1128/mcb.02187-06] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Phosphorylation of the C-terminal domain (CTD) of RNA polymerase II (RNAP II) is a dynamic process that regulates transcription and coordinates it with pre-mRNA processing. We show here that Rct1, a nuclear multidomain cyclophilin from Schizosaccharomyces pombe, is encoded by an essential gene that interacts with the CTD and regulates its phosphorylation in vivo. Downregulation of Rct1 levels results in increased phosphorylation of the CTD at both Ser2 and Ser5 and in a commensurate decrease in RNAP II transcription. In contrast, overexpression of Rct1 decreases phosphorylation on both sites. The close association of Rct1 with transcriptionally active chromatin suggests a role in regulation of RNAP II transcriptional activity. These data, together with the pleiotropic phenotype upon Rct1 deregulation, suggest that this multidomain cyclophilin is an important player in maintaining the correct phosphorylation code of the CTD and thereby regulating CTD function.
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Affiliation(s)
- Monika Gullerova
- Max F. Perutz Laboratories, Medical University of Vienna, Department of Medical Biochemistry, Bohrgasse 9/3, A-1030 Vienna, Austria
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31
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Palusa SG, Ali GS, Reddy ASN. Alternative splicing of pre-mRNAs of Arabidopsis serine/arginine-rich proteins: regulation by hormones and stresses. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 49:1091-107. [PMID: 17319848 DOI: 10.1111/j.1365-313x.2006.03020.x] [Citation(s) in RCA: 282] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Precursor mRNAs with introns can undergo alternative splicing (AS) to produce structurally and functionally different proteins from the same gene. Here, we show that the pre-mRNAs of Arabidopsis genes that encode serine/arginine-rich (SR) proteins, a conserved family of splicing regulators in eukaryotes, are extensively alternatively spliced. Remarkably about 95 transcripts are produced from only 15 genes, thereby increasing the complexity of the SR gene family transcriptome by six-fold. The AS of some SR genes is controlled in a developmental and tissue-specific manner. Interestingly, among the various hormones and abiotic stresses tested, temperature stress (cold and heat) dramatically altered the AS of pre-mRNAs of several SR genes, whereas hormones altered the splicing of only three SR genes. These results indicate that abiotic stresses regulate the AS of the pre-mRNAs of SR genes to produce different isoforms of SR proteins that are likely to have altered function(s) in pre-mRNA splicing. Sequence analysis of splice variants revealed that predicted proteins from a majority of these variants either lack one or more modular domains or contain truncated domains. Because of the modular nature of the various domains in SR proteins, the proteins produced from splice variants are likely to have distinct functions. Together our results indicate that Arabidopsis SR genes generate surprisingly large transcriptome complexity, which is altered by stresses and hormones.
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32
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Fic W, Juge F, Soret J, Tazi J. Eye development under the control of SRp55/B52-mediated alternative splicing of eyeless. PLoS One 2007; 2:e253. [PMID: 17327915 PMCID: PMC1803029 DOI: 10.1371/journal.pone.0000253] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2007] [Accepted: 01/31/2007] [Indexed: 11/18/2022] Open
Abstract
The genetic programs specifying eye development are highly conserved during evolution and involve the vertebrate Pax-6 gene and its Drosophila melanogaster homolog eyeless (ey). Here we report that the SR protein B52/SRp55 controls a novel developmentally regulated splicing event of eyeless that is crucial for eye growth and specification in Drosophila. B52/SRp55 generates two isoforms of eyeless differing by an alternative exon encoding a 60-amino-acid insert at the beginning of the paired domain. The long isoform has impaired ability to trigger formation of ectopic eyes and to bind efficiently Eyeless target DNA sequences in vitro. When over-produced in the eye imaginal disc, this isoform induces a small eye phenotype, whereas the isoform lacking the alternative exon triggers eye over-growth and strong disorganization. Our results suggest that B52/SRp55 splicing activity is used during normal eye development to control eye organogenesis and size through regulation of eyeless alternative splicing.
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Affiliation(s)
- Weronika Fic
- Institut de Génétique Moléculaire de Montpellier (IGMM), UMR 5535, Université de Montpellier II, Centre National de Recherche Scientifique (CNRS), Montpellier, France
| | - François Juge
- Institut de Génétique Moléculaire de Montpellier (IGMM), UMR 5535, Université de Montpellier II, Centre National de Recherche Scientifique (CNRS), Montpellier, France
| | - Johann Soret
- Institut de Génétique Moléculaire de Montpellier (IGMM), UMR 5535, Université de Montpellier II, Centre National de Recherche Scientifique (CNRS), Montpellier, France
| | - Jamal Tazi
- Institut de Génétique Moléculaire de Montpellier (IGMM), UMR 5535, Université de Montpellier II, Centre National de Recherche Scientifique (CNRS), Montpellier, France
- * To whom correspondence should be addressed. E-mail:
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33
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Singh OP, Visa N, Wieslander L, Daneholt B. A specific SR protein binds preferentially to the secretory protein gene transcripts in salivary glands of Chironomus tentans. Chromosoma 2006; 115:449-58. [PMID: 16858590 DOI: 10.1007/s00412-006-0073-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2006] [Revised: 05/20/2006] [Accepted: 05/22/2006] [Indexed: 11/26/2022]
Abstract
The members of the serine-arginine (SR) family of proteins play multiple roles in posttranscriptional gene expression. Initially considered as essential splicing factors confined to the nucleus and regulating constitutive and alternative splicing, SR proteins are now known to shuttle between the nucleus and the cytoplasm and to be involved in mRNA biogenesis, transport, and translation. In Chironomus tentans, hrp45 is an SR protein structurally similar to the Drosophila SRp55/B52 SR protein. We have studied how hrp45, hrp36 [a heterogenous nuclear ribonucleoprotein (hnRNP) protein], and small nuclear RNP (snRNP) proteins are distributed in the transcriptionally active loci of polytene chromosomes in C. tentans. Immunofluorescence visualization of the proteins in double-labeling experiments revealed that hrp45 preferentially associates with a small number of puffs. On the other hand, hrp36 and snRNP proteins were found distributed in a large number of loci with little quantitative difference. Remarkably, hrp45-labeled loci coincide with the sites of transcription of premessenger RNPs of secretory protein (sp) genes. Because the labeling was found sensitive to RNase A treatment, we conclude that the SR protein hrp45 preferentially binds to sp gene transcripts in salivary gland cells. The preferential association of a specific SR protein with a particular type of gene transcripts reflects substrate-specific function(s) of an SR protein, in vivo. The possible roles that hrp45 might be playing in speedy and efficient processing of sp gene transcripts are discussed.
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Affiliation(s)
- Om Prakash Singh
- Department of Cell and Molecular Biology, Medical Nobel Institute, Karolinska Institutet, Stockholm, 171 77, Sweden
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34
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Shen H, Green MR. RS domains contact splicing signals and promote splicing by a common mechanism in yeast through humans. Genes Dev 2006; 20:1755-65. [PMID: 16766678 PMCID: PMC1522072 DOI: 10.1101/gad.1422106] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Serine-arginine (SR) proteins are general metazoan splicing factors that contain an essential arginine-serine-rich (RS) domain. We have previously found that mammalian spliceosome assembly involves a series of sequential interactions between RS domains and two splicing signals: the branchpoint and the 5' splice site. Here we study how RS domains are directed to specifically contact splicing signals, and how this interaction promotes splicing. The yeast Saccharomyces cerevisiae lacks SR proteins. However, we show that tethering a mammalian RS domain to a yeast actin pre-mRNA rescues splicing of certain branchpoint or 5' splice site mutants in which U snRNA base-pairing has been decreased. Conversely, on a mammalian pre-mRNA, a normally essential SR protein becomes dispensable when the complementarity of a splicing signal to a U snRNA is increased. We find that in the absence of other splicing factors an RS domain tethered to a pre-mRNA selectively contacts a double-stranded RNA region and enhances RNA-RNA base-pairing. Significantly, all of these activities require phosphorylation of the RS domain. Based on these results, we propose that RS domains selectively contact splicing signals because, due to transient U snRNA base-pairing, they are partially double-stranded. The RS domain-splicing signal interaction, in turn, promotes (or stabilizes) base-pairing between the U snRNA and pre-mRNA substrate, thereby enhancing splicing. Our results reveal a common mechanism of RS domain function in yeast through humans.
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MESH Headings
- Arginine/genetics
- Arginine/metabolism
- Base Pairing
- Evolution, Molecular
- Humans
- Mutation
- Phosphorylation
- Protein Serine-Threonine Kinases/physiology
- Protein Structure, Tertiary
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA Splicing/genetics
- RNA Splicing/physiology
- RNA, Double-Stranded/genetics
- RNA, Double-Stranded/physiology
- RNA, Fungal/genetics
- RNA, Fungal/physiology
- RNA, Small Nuclear/genetics
- RNA, Small Nuclear/physiology
- Ribonucleoproteins, Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/physiology
- Saccharomyces cerevisiae Proteins/physiology
- Serine/genetics
- Serine/metabolism
- Spliceosomes/genetics
- Spliceosomes/physiology
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Affiliation(s)
- Haihong Shen
- Howard Hughes Medical Institute and Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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35
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Gullerova M, Barta A, Lorkovic ZJ. AtCyp59 is a multidomain cyclophilin from Arabidopsis thaliana that interacts with SR proteins and the C-terminal domain of the RNA polymerase II. RNA (NEW YORK, N.Y.) 2006; 12:631-43. [PMID: 16497658 PMCID: PMC1421086 DOI: 10.1261/rna.2226106] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
AtCyp59 and its orthologs from different organisms belong to a family of modular proteins consisting of a peptidyl-prolyl cis-trans isomerase (PPIase) domain, followed by an RNA recognition motif (RRM), and a C-terminal domain enriched in charged amino acids. AtCyp59 was identified in a yeast two-hybrid screen as an interacting partner of the Arabidopsis SR protein SCL33/SR33. The interaction with SCL33/SR33 and with a majority of Arabidopsis SR proteins was confirmed by in vitro pull-down assays. Consistent with these interactions, AtCyp59 localizes to the cell nucleus, but it does not significantly colocalize with SR proteins in nuclear speckles. Rather, it shows a punctuate localization pattern resembling transcription sites. Indeed, by using yeast two-hybrid, in vitro pull-down, and immunoprecipitation assays, we found that AtCyp59 interacts with the C-terminal domain (CTD) of the largest subunit of RNA polymerase II. Ectopic expression of the tagged protein in Arabidopsis cell suspension resulted in highly reduced growth that is most probably due to reduced phosphorylation of the CTD. Together our data suggest a possible function of AtCyp59 in activities connecting transcription and pre-mRNA processing. We discuss our data in the context of a dynamic interplay between transcription and pre-mRNA processing.
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Affiliation(s)
- Monika Gullerova
- Max F. Perutz Laboratories, University Departments at the Vienna Biocenter, Department of Biochemistry, Medical University of Vienna, Dr. Bohrgasse 9/3, A-1030 Vienna, Austria
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36
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Delaney KJ, Xu R, Zhang J, Li QQ, Yun KY, Falcone DL, Hunt AG. Calmodulin interacts with and regulates the RNA-binding activity of an Arabidopsis polyadenylation factor subunit. PLANT PHYSIOLOGY 2006; 140:1507-21. [PMID: 16500995 PMCID: PMC1459842 DOI: 10.1104/pp.105.070672] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The Arabidopsis (Arabidopsis thaliana) gene that encodes the probable ortholog of the 30-kD subunit of the mammalian cleavage and polyadenylation specificity factor (CPSF) is a complex one, encoding small (approximately 28 kD) and large (approximately 68 kD) polypeptides. The small polypeptide (AtCPSF30) corresponds to CPSF30 and is the focus of this study. Recombinant AtCPSF30 was purified from Escherichia coli and found to possess RNA-binding activity. Mutational analysis indicated that an evolutionarily conserved central core of AtCPSF30 is involved in RNA binding, but that RNA binding also requires a short sequence adjacent to the N terminus of the central core. AtCPSF30 was found to bind calmodulin, and calmodulin inhibited the RNA-binding activity of the protein in a calcium-dependent manner. Mutational analysis showed that a small part of the protein, again adjacent to the N terminus of the conserved core, is responsible for calmodulin binding; point mutations in this region abolished both binding to and inhibition of RNA binding by calmodulin. Interestingly, AtCPSF30 was capable of self-interactions. This property also mapped to the central conserved core of the protein. However, calmodulin had no discernible effect on the self-association. These results show that the central portion of AtCPSF30 is involved in a number of important functions, and they raise interesting possibilities for both the interplay between splicing and polyadenylation and the regulation of these processes by stimuli that act through calmodulin.
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Affiliation(s)
- Kimberly J Delaney
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, Kentucky 40546-0312, USA
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37
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Soret J, Gabut M, Tazi J. SR Proteins as Potential Targets for Therapy. ALTERNATIVE SPLICING AND DISEASE 2006; 44:65-87. [PMID: 17076265 DOI: 10.1007/978-3-540-34449-0_4] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Serine- and arginine-rich (SR) proteins constitute a highly conserved family of pre-mRNA splicing factors that play key roles in the regulation of splice site selection, and thereby in the control of alternative splicing processes. In addition to conserved sequences at the splice junctions, splice site selection also depends upon different sets of auxiliary cis regulatory elements known as exonic and intronic splicing enhancers (ESEs and ISEs) or exonic and intronic silencers (ESSs and ISSs). Specific binding of SR proteins to their cognate splicing enhancers as well as binding of splicing repressor to silencer sequences serve to enhance or inhibit recognition of weak splice sites by the splicing machinery. Given that the vast majority of human genes contain introns and that most pre-mRNAs containing multiple exons undergo alternative splicing, mutations disrupting or creating such auxiliary elements can result in aberrant splicing events at the origin of various human diseases. In the past few years, numerous studies have reported several approaches allowing correction of such aberrant splicing events by targeting either the mutated sequences or the splicing regulators whose binding is affected by the mutation. The aim of the present review is to highlight the different means by which it is possible to modulate the activity of SR splicing factors and to bring out those holding the greatest promises for the development of therapeutic treatments.
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Affiliation(s)
- Johann Soret
- Institut de Génétique Moléculaire de Montpellier, UMR 5535, IFR 122, Centre National de Recherche Scientifique, 1919, route de Mende, 34293 Montpellier, France
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38
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Cazalla D, Sanford JR, Cáceres JF. A rapid and efficient protocol to purify biologically active recombinant proteins from mammalian cells. Protein Expr Purif 2005; 42:54-8. [PMID: 15878828 DOI: 10.1016/j.pep.2005.03.035] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2004] [Revised: 03/24/2005] [Accepted: 03/30/2005] [Indexed: 11/15/2022]
Abstract
Here, we describe a simple and efficient method for the expression and purification of active recombinant proteins in mammalian cells. This method uses the expression of T7 epitope-tagged proteins in transiently transfected 293T cells grown in monolayer, followed by anti-T7-agarose affinity chromatography. This procedure yields approximately between 75 and 100 microg of biologically active protein/150 cm(2) flask that can be used for biochemical studies. We have tested this protocol for the expression of the prototype SR protein, SF2/ASF, which is a member of the SR protein family with a role in constitutive and alternative splicing. We show that SF2/ASF purified using this protocol is able to complement an S100 HeLa extract, demonstrating that is biologically active. Moreover, expression of a novel SR-related protein that it is required for the second step of pre-mRNA splicing also rendered an active protein. In summary, we present a protocol based on transient transfection of mammalian cells that results in easy purification of significant amounts of biologically active proteins.
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39
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Abstract
Pre-mRNA splicing is catalyzed by two unique spliceosomes, designated U2- or U12-dependent. In contrast to the well-characterized U2-dependent spliceosome, much remains to be learned about the less abundant U12-type spliceosome. This review focuses on recent advances in elucidating the structure and function of the minor U12-dependent spliceosome. Interesting similarities and differences between the U12- and U2-dependent spliceosomes are also highlighted.
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Affiliation(s)
- Cindy L Will
- Max Planck Institute for Biophysical Chemistry, Department of Cellular Biochemistry, Am Fassberg 11, D-37077 Göttingen, Germany.
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40
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Li X, Wang J, Manley JL. Loss of splicing factor ASF/SF2 induces G2 cell cycle arrest and apoptosis, but inhibits internucleosomal DNA fragmentation. Genes Dev 2005; 19:2705-14. [PMID: 16260492 PMCID: PMC1283963 DOI: 10.1101/gad.1359305] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
ASF/SF2 is an SR protein splicing factor that participates in constitutive and alternative pre-mRNA splicing and is essential for cell viability. Using a genetically modified chicken B-cell line, DT40-ASF, we now show that ASF/SF2 inactivation results in a G2-phase cell cycle arrest and subsequent programmed cell death. However, although several hallmarks of apoptosis are apparent, internucleosomal DNA fragmentation was not detected. Furthermore, inactivation of ASF/SF2 also blocks DNA fragmentation normally induced by a variety of apoptotic stimuli. Notably, mRNA encoding the inhibitor of caspase-activated DNase-L (ICAD-L), which acts as an inhibitor as well as a chaperone of caspase-activated DNase (CAD), decreased in abundance, whereas the level of mRNA encoding ICAD-S, which has only inhibitory activity, increased upon ASF/SF2 depletion. Strikingly, expression of appropriate levels of exogenous human ICAD-L restored apoptotic DNA laddering in ASF/SF2-depleted cells. These results not only indicate that loss of an SR protein splicing factor can induce cell cycle arrest and apoptosis, but also illustrate the important role of ICAD and its regulation by alternative splicing in the process of apoptotic DNA fragmentation.
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Affiliation(s)
- Xialu Li
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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41
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Björk P, Wetterberg-Strandh I, Baurén G, Wieslander L. Chironomus tentans-repressor splicing factor represses SR protein function locally on pre-mRNA exons and is displaced at correct splice sites. Mol Biol Cell 2005; 17:32-42. [PMID: 16236800 PMCID: PMC1345644 DOI: 10.1091/mbc.e05-04-0339] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Chironomus tentans-repressor splicing factor (Ct-RSF) represses the activation of splicing by SR proteins in vitro. Ct-RSF colocalizes with the Ser-Arg-rich (SR) protein hrp45 in interchromatin granule clusters and coimmunoprecipitates with hrp45 in nuclear extracts. Ct-RSF and hrp45 can also interact directly in vitro. Ct-RSF and hrp45 are recruited together to transcribing genes and associate with growing pre-mRNAs. Ct-RSF and hrp45 colocalize at a large number of gene loci. Injection of anti-Ct-RSF antibodies into nuclei of living cells blocks association of both Ct-RSF and hrp45 with the growing pre-mRNA, whereas binding of U2 small nuclear ribonucleoprotein particle (snRNP) to the pre-mRNA is unaffected. On the intron-rich Balbiani ring (BR) 3 pre-mRNA, hrp45 as well as U1 and U2 snRNPs bind extensively, whereas relatively little Ct-RSF is present. In contrast, the BR1 and BR2 pre-mRNAs, dominated by exon sequences, bind relatively much Ct-RSF compared with hrp45 and snRNPs. Our data suggest that Ct-RSF represses SR protein function at exons and that the assembly of spliceosomes at authentic splice sites displaces Ct-RSF locally.
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Affiliation(s)
- Petra Björk
- Department of Molecular Biology and Functional Genomics, Stockholm University, SE-106 91 Stockholm, Sweden
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42
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Shaw BD, Upadhyay S. Aspergillus nidulans swoK encodes an RNA binding protein that is important for cell polarity. Fungal Genet Biol 2005; 42:862-72. [PMID: 16098776 DOI: 10.1016/j.fgb.2005.06.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2005] [Revised: 06/05/2005] [Accepted: 06/08/2005] [Indexed: 10/25/2022]
Abstract
The Aspergillus nidulans swoK1 mutant is defective in polarity maintenance when grown at restrictive temperature (38 degrees C). Upon germination, the mutant extends a primary germ tube that swells to an enlarged, non-uniform cell with pronounced wall thickenings. The mutant is fully restored to wild-type growth when transformed with a plasmid containing the AN5802.2 ORF as designated in The Broad Institute A. nidulans sequence database. Genetic mapping places swoK in the same region of chromosome I, as that occupied by An5802.2 on the physical map. swoK is predicted to encode a protein that contains an N-terminal RRM (RNA Recognition Motif) and a highly repetitive C-terminus with numerous RD/DR and RS/SR dipeptides. We hypothesize that SwoK participates in one of the known functions of SR proteins (those that contain SR/RS repeats): mRNA maturation through the spliceosome and or transport of mRNAs out of the nucleus to sites of protein translation.
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Affiliation(s)
- Brian D Shaw
- Program for the Biology of Filamentous Fungi, Department of Plant Pathology and Microbiology, Texas A and M University, 2132 TAMU, College Station, TX 77843, USA.
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43
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Li X, Manley JL. Inactivation of the SR protein splicing factor ASF/SF2 results in genomic instability. Cell 2005; 122:365-78. [PMID: 16096057 DOI: 10.1016/j.cell.2005.06.008] [Citation(s) in RCA: 572] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2004] [Revised: 01/18/2005] [Accepted: 06/06/2005] [Indexed: 01/10/2023]
Abstract
SR proteins constitute a family of pre-mRNA splicing factors now thought to play several roles in mRNA metabolism in metazoan cells. Here we provide evidence that a prototypical SR protein, ASF/SF2, is unexpectedly required for maintenance of genomic stability. We first show that in vivo depletion of ASF/SF2 results in a hypermutation phenotype likely due to DNA rearrangements, reflected in the rapid appearance of DNA double-strand breaks and high-molecular-weight DNA fragments. Analysis of DNA from ASF/SF2-depleted cells revealed that the nontemplate strand of a transcribed gene was single stranded due to formation of an RNA:DNA hybrid, R loop structure. Stable overexpression of RNase H suppressed the DNA-fragmentation and hypermutation phenotypes. Indicative of a direct role, ASF/SF2 prevented R loop formation in a reconstituted in vitro transcription reaction. Our results support a model by which recruitment of ASF/SF2 to nascent transcripts by RNA polymerase II prevents formation of mutagenic R loop structures.
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Affiliation(s)
- Xialu Li
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
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44
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Sanford JR, Ellis J, Cáceres JF. Multiple roles of arginine/serine-rich splicing factors in RNA processing. Biochem Soc Trans 2005; 33:443-6. [PMID: 15916537 DOI: 10.1042/bst0330443] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
SR proteins (serine- and arginine-rich proteins) are an evolutionarily conserved family consisting of essential pre-mRNA splicing factors. Since their discovery and initial characterization, roles of SR proteins in pre-mRNA splicing and in subsequent steps of post-transcriptional gene expression have expanded significantly. The current hypotheses suggest that SR proteins are multifunctional adaptor molecules that may couple distinct steps of RNA metabolism. In the present study, we will provide an overview of the roles of SR proteins in different steps of post-transcriptional gene expression.
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Affiliation(s)
- J R Sanford
- MRC Human Genetics Unit, Edinburgh EH4 2XU, Scotland, U.K
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45
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Venables JP, Bourgeois CF, Dalgliesh C, Kister L, Stevenin J, Elliott DJ. Up-regulation of the ubiquitous alternative splicing factor Tra2β causes inclusion of a germ cell-specific exon. Hum Mol Genet 2005; 14:2289-303. [PMID: 16000324 DOI: 10.1093/hmg/ddi233] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We have discovered a new exon of the homeodomain-interacting kinase HipK3 that incorporates a premature stop codon and is included only in the human testis. To investigate this, we tested the effects of transfecting cells with green fluorescent protein fusions of RNA-binding proteins implicated in spermatogenesis using a novel assay based on multi-fraction fluorescence-activated cell sorting (MF-FACS). This allows the effect of a controlled titration of any splicing factor on the splicing of endogenous genes to be studied in vivo. We found that Tra2beta recapitulates testis-specific splicing of endogenous HipK3 in a concentration-dependent manner and binds specifically to a long purine-rich sequence in the novel exon. This sequence was also specifically bound by hnRNP A1, hnRNP H, ASF/SF2 and SRp40, but not by 9G8. Consistent with these observations, in vitro studies showed that this sequence shifts splicing to a downstream 5' splice site within a heterologous pre-mRNA substrate in the presence of Tra2beta, ASF/SF2 and SRp40, whereas hnRNP A1 specifically inhibits this choice. By mutating the purine-rich sequence in the context of the HipK3 gene, we also show that it is the major determinant of Tra2beta- and hnRNP A1-mediated regulation. Tra2 is essential for sex determination and spermatogenesis in flies, and Tra2beta protein was most highly expressed in testis out of six mouse tissues, whereas hnRNP A1 is down-regulated during germ cell development. Therefore, our data imply an evolutionarily conserved role for Tra2 proteins in spermatogenesis and suggest that an elevated concentration of Tra2beta may convert it into a tissue-specific splicing factor.
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Affiliation(s)
- Julian P Venables
- Institute of Human Genetics, University of Newcastle upon Tyne, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK.
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46
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Auboeuf D, Dowhan DH, Dutertre M, Martin N, Berget SM, O'Malley BW. A subset of nuclear receptor coregulators act as coupling proteins during synthesis and maturation of RNA transcripts. Mol Cell Biol 2005; 25:5307-16. [PMID: 15964789 PMCID: PMC1156981 DOI: 10.1128/mcb.25.13.5307-5316.2005] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Didier Auboeuf
- INSERM U685/AVENIR, Centre G. Hayem, Hôpital Saint Louis, Paris, France.
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47
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Metz A, Soret J, Vourc'h C, Tazi J, Jolly C. A key role for stress-induced satellite III transcripts in the relocalization of splicing factors into nuclear stress granules. J Cell Sci 2005; 117:4551-8. [PMID: 15331664 DOI: 10.1242/jcs.01329] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Exposure of cells to stressful conditions results in the rapid synthesis of a subset of specialized proteins termed heat shock proteins (HSPs) which function in protecting the cell against damage. The stress-induced activation of hsp genes is controlled by the heat shock transcription factor 1 (HSF1). At the cellular level, one of the most striking effects of stress is the rapid and reversible redistribution of HSF1 into a few nuclear structures termed nuclear stress granules which form primarily on the 9q12 locus in humans. Within these structures, HSF1 binds to satellite III repeated elements and drives the RNA polymerase II-dependent transcription of these sequences into stable RNAs which remain associated with the 9q12 locus for a certain time after synthesis. Other proteins, in particular splicing factors, were also shown to relocalize to the granules upon stress. Here, we investigated the role of stress-induced satellite III transcripts in the relocalization of splicing factors to the granules. We show that the recruitment of the two serine/arginine-rich (SR) proteins SF2/ASF and SRp30c requires the presence of stress-induced satellite III transcripts. In agreement with these findings, we identified the second RNA-recognition motif (RRM2) of hSF2/ASF as the motif required for the targeting to the granules, and we showed by immunoprecipitation that the endogenous hSF2/ASF protein is present in a complex with satellite III transcripts in stressed cells in vivo. Interestingly, satellite III transcripts also immunoprecipitate together with small nuclear ribonucleoproteins (snRNPs) in vivo whereas the intronless hsp70 transcripts do not, supporting the proposal that these transcripts are subject to splicing. Altogether, these data highlight the central role for satellite III transcripts in the targeting and/or retention of splicing factors into the granules upon stress.
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Affiliation(s)
- Alexandra Metz
- INSERM U309, Institut Albert Bonniot, Domaine de la Merci, 38706 La Tronche CEDEX, France
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48
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D'Souza I, Schellenberg GD. Regulation of tau isoform expression and dementia. Biochim Biophys Acta Mol Basis Dis 2005; 1739:104-15. [PMID: 15615630 DOI: 10.1016/j.bbadis.2004.08.009] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2004] [Accepted: 08/24/2004] [Indexed: 10/26/2022]
Abstract
In the central nervous system (CNS), aberrant changes in tau mRNA splicing and consequently in protein isoform ratios cause abnormal aggregation of tau and neurodegeneration. Pathological tau causes neuronal loss in Alzheimer's disease (AD) and a diverse group of disorders called the frontotemporal dementias (FTD), which are two of the most common forms of dementia and afflict more than 10% of the elderly population. Autosomal dominant mutations in the tau gene cause frontotemporal dementia with parkinsonism-chromosome 17 type (FTDP-17). Just over half the mutations affect tau protein function and decrease its affinity for microtubules (MTs) or increase self-aggregation. The remaining mutations occur within exon 10 (E10) and intron 10 sequences and alter complex regulation of E10 splicing by multiple mechanisms. FTDP-17 splicing mutations disturb the normally balanced levels of distinct protein isoforms that result in altered biochemical and structural properties of tau. In addition to FTDP-17, altered tau isoform levels are also pathogenically associated with other FTD disorders such as progressive supranuclear palsy (PSP), corticobasal degeneration and Pick's disease; however, the mechanisms remain undefined and mutations in tau have not been detected. FTDP-17 highlights the association between splicing mutations and the pronounced variability in pathology as well as phenotype that is characteristic of inherited disorders.
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Affiliation(s)
- Ian D'Souza
- Geriatric Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle Division, 1660 S. Columbian Way, Seattle, WA 98108, USA
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49
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Caputi M, Freund M, Kammler S, Asang C, Schaal H. A bidirectional SF2/ASF- and SRp40-dependent splicing enhancer regulates human immunodeficiency virus type 1 rev, env, vpu, and nef gene expression. J Virol 2004; 78:6517-26. [PMID: 15163745 PMCID: PMC416506 DOI: 10.1128/jvi.78.12.6517-6526.2004] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The integrated human immunodeficiency virus type 1 (HIV-1) genome is transcribed in a single pre-mRNA that is alternatively spliced into more than 40 mRNAs. We characterized a novel bidirectional exonic splicing enhancer (ESE) that regulates the expression of the HIV-1 env, vpu, rev, and nef mRNAs. The ESE is localized downstream of the vpu-, env-, and nef-specific 3' splice site no. 5. SF2/ASF and SRp40 activate the ESE and are required for efficient 3' splice site usage and binding of the U1 snRNP to the downstream 5' splice site no. 4. U1 snRNP binding to the 5' splice site no. 4 is required for splicing of the rev and nef mRNAs and to increase expression of the partially spliced env mRNA. Finally, our results indicate that this ESE is necessary for the recruitment of the U1 snRNP to the 5' splice site no. 4, even when the 5' splice site and the U1 snRNA have been mutated to obtain a perfect complementary match. The ESE characterized here is highly conserved in most viral subtypes.
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MESH Headings
- Base Sequence
- Enhancer Elements, Genetic
- Exons
- Gene Expression Regulation, Viral
- Gene Products, env/genetics
- Gene Products, env/metabolism
- Gene Products, nef/genetics
- Gene Products, nef/metabolism
- Gene Products, rev/genetics
- Gene Products, rev/metabolism
- HIV-1/classification
- HIV-1/genetics
- HIV-1/physiology
- HeLa Cells
- Human Immunodeficiency Virus Proteins
- Humans
- Molecular Sequence Data
- Nuclear Proteins/metabolism
- Phosphoproteins/metabolism
- RNA Splicing
- RNA, Messenger/biosynthesis
- RNA, Viral/biosynthesis
- RNA-Binding Proteins
- Ribonucleoprotein, U1 Small Nuclear/metabolism
- Serine-Arginine Splicing Factors
- Spliceosomes
- Viral Regulatory and Accessory Proteins/genetics
- Viral Regulatory and Accessory Proteins/metabolism
- nef Gene Products, Human Immunodeficiency Virus
- rev Gene Products, Human Immunodeficiency Virus
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Affiliation(s)
- Massimo Caputi
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
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Sanford JR, Gray NK, Beckmann K, Cáceres JF. A novel role for shuttling SR proteins in mRNA translation. Genes Dev 2004; 18:755-68. [PMID: 15082528 PMCID: PMC387416 DOI: 10.1101/gad.286404] [Citation(s) in RCA: 289] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The Ser-Arg-rich (SR) proteins comprise a large family of nuclear phosphoproteins that are required for constitutive and alternative splicing. A subset of SR proteins shuttles continuously between the nucleus and the cytoplasm, suggesting that the role of shuttling SR proteins in gene expression may not be limited to nuclear pre-mRNA splicing, but may also include unknown cytoplasmic functions. Here, we show that shuttling SR proteins, in particular SF2/ASF, associate with translating ribosomes and stimulate translation when tethered to a reporter mRNA in Xenopus oocytes. Moreover, SF2/ASF enhances translation of reporter mRNAs in HeLa cells, and this activity is dependent on its ability to shuttle from the nucleus to the cytoplasm and is increased by the presence of an exonic-splicing enhancer. Furthermore, SF2/ASF can stimulate translation in vitro using a HeLa cell-free translation system. Thus, the association of SR proteins with translating ribosomes, as well as the stimulation of translation both in vivo and in vitro, strongly suggest a role for shuttling SR proteins in translation. We propose that shuttling SR proteins play multiple roles in the posttranscriptional expression of eukaryotic genes and illustrate how they may couple splicing and translation.
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Affiliation(s)
- Jeremy R Sanford
- Medical Research Council Human Genetics Unit, Western General Hospital, Edinburgh EH4 2XU, Scotland, United Kingdom
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