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Sertznig H, Hillebrand F, Erkelenz S, Schaal H, Widera M. Behind the scenes of HIV-1 replication: Alternative splicing as the dependency factor on the quiet. Virology 2018; 516:176-188. [PMID: 29407375 DOI: 10.1016/j.virol.2018.01.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/10/2018] [Accepted: 01/11/2018] [Indexed: 01/31/2023]
Abstract
Alternative splicing plays a key role in the HIV-1 life cycle and is essential to maintain an equilibrium of mRNAs that encode viral proteins and polyprotein-isoforms. In particular, since all early HIV-1 proteins are expressed from spliced intronless and late enzymatic and structural proteins from intron containing, i.e. splicing repressed viral mRNAs, cellular splicing factors and splicing regulatory proteins are crucial for the replication capacity. In this review, we will describe the complex network of cis-acting splicing regulatory elements (SREs), which are mainly localized in the neighbourhoods of all HIV-1 splice sites and warrant the proper ratio of individual transcript isoforms. Since SREs represent binding sites for trans-acting cellular splicing factors interacting with the cellular spliceosomal apparatus we will review the current knowledge of interactions between viral RNA and cellular proteins as well as their impact on viral replication. Finally, we will discuss potential therapeutic approaches targeting HIV-1 alternative splicing.
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Affiliation(s)
- Helene Sertznig
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Frank Hillebrand
- Institute of Virology, Heinrich Heine University, University Hospital, Düsseldorf, Germany
| | - Steffen Erkelenz
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Germany
| | - Heiner Schaal
- Institute of Virology, Heinrich Heine University, University Hospital, Düsseldorf, Germany
| | - Marek Widera
- Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.
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2
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Characterizing HIV-1 Splicing by Using Next-Generation Sequencing. J Virol 2017; 91:JVI.02515-16. [PMID: 28077653 DOI: 10.1128/jvi.02515-16] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 01/04/2017] [Indexed: 02/07/2023] Open
Abstract
Full-length human immunodeficiency virus type 1 (HIV-1) RNA serves as the genome or as an mRNA, or this RNA undergoes splicing using four donors and 10 acceptors to create over 50 physiologically relevant transcripts in two size classes (1.8 kb and 4 kb). We developed an assay using Primer ID-tagged deep sequencing to quantify HIV-1 splicing. Using the lab strain NL4-3, we found that A5 (env/nef) is the most commonly used acceptor (about 50%) and A3 (tat) the least used (about 3%). Two small exons are made when a splice to acceptor A1 or A2 is followed by activation of donor D2 or D3, and the high-level use of D2 and D3 dramatically reduces the amount of vif and vpr transcripts. We observed distinct patterns of temperature sensitivity of splicing to acceptors A1 and A2. In addition, disruption of a conserved structure proximal to A1 caused a 10-fold reduction in all transcripts that utilized A1. Analysis of a panel of subtype B transmitted/founder viruses showed that splicing patterns are conserved, but with surprising variability of usage. A subtype C isolate was similar, while a simian immunodeficiency virus (SIV) isolate showed significant differences. We also observed transsplicing from a downstream donor on one transcript to an upstream acceptor on a different transcript, which we detected in 0.3% of 1.8-kb RNA reads. There were several examples of splicing suppression when the env intron was retained in the 4-kb size class. These results demonstrate the utility of this assay and identify new examples of HIV-1 splicing regulation. IMPORTANCE During HIV-1 replication, over 50 conserved spliced RNA variants are generated. The splicing assay described here uses new developments in deep-sequencing technology combined with Primer ID-tagged cDNA primers to efficiently quantify HIV-1 splicing at a depth that allows even low-frequency splice variants to be monitored. We have used this assay to examine several features of HIV-1 splicing and to identify new examples of different mechanisms of regulation of these splicing patterns. This splicing assay can be used to explore in detail how HIV-1 splicing is regulated and, with moderate throughput, could be used to screen for structural elements, small molecules, and host factors that alter these relatively conserved splicing patterns.
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3
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Lopez-Mejia IC, Vautrot V, De Toledo M, Behm-Ansmant I, Bourgeois CF, Navarro CL, Osorio FG, Freije JMP, Stévenin J, De Sandre-Giovannoli A, Lopez-Otin C, Lévy N, Branlant C, Tazi J. A conserved splicing mechanism of the LMNA gene controls premature aging. Hum Mol Genet 2011; 20:4540-55. [PMID: 21875900 DOI: 10.1093/hmg/ddr385] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Hutchinson-Gilford progeria syndrome (HGPS) is a rare genetic disorder phenotypically characterized by many features of premature aging. Most cases of HGPS are due to a heterozygous silent mutation (c.1824C>T; p.Gly608Gly) that enhances the use of an internal 5' splice site (5'SS) in exon 11 of the LMNA pre-mRNA and leads to the production of a truncated protein (progerin) with a dominant negative effect. Here we show that HGPS mutation changes the accessibility of the 5'SS of LMNA exon 11 which is sequestered in a conserved RNA structure. Our results also reveal a regulatory role of a subset of serine-arginine (SR)-rich proteins, including serine-arginine rich splicing factor 1 (SRSF1) and SRSF6, on utilization of the 5'SS leading to lamin A or progerin production and a modulation of this regulation in the presence of the c.1824C>T mutation is shown directly on HGPS patient cells. Mutant mice carrying the equivalent mutation in the LMNA gene (c.1827C>T) also accumulate progerin and phenocopy the main cellular alterations and clinical defects of HGPS patients. RNAi-induced depletion of SRSF1 in the HGPS-like mouse embryonic fibroblasts (MEFs) allowed progerin reduction and dysmorphic nuclei phenotype correction, whereas SRSF6 depletion aggravated the HGPS-like MEF's phenotype. We demonstrate that changes in the splicing ratio between lamin A and progerin are key factors for lifespan since heterozygous mice harboring the mutation lived longer than homozygous littermates but less than the wild-type. Genetic and biochemical data together favor the view that physiological progerin production is under tight control of a conserved splicing mechanism to avoid precocious aging.
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Affiliation(s)
- Isabel C Lopez-Mejia
- CNRS, UMR 5535, University of Montpellier, Institut de Génétique Moléculaire de Montpellier, 1919 Route de Mende, Montpellier 34293, France
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4
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Bar A, Marchand V, Khoury G, Dreumont N, Mougin A, Robas N, Stévenin J, Visvikis A, Branlant C. Structural and functional analysis of the Rous Sarcoma virus negative regulator of splicing and demonstration of its activation by the 9G8 SR protein. Nucleic Acids Res 2010; 39:3388-403. [PMID: 21183462 PMCID: PMC3082916 DOI: 10.1093/nar/gkq1114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Retroviruses require both spliced and unspliced RNAs for replication. Accumulation of Rous Sarcoma virus (RSV) unspliced RNA depends upon the negative regulator of splicing (NRS). Its 5′-part is considered as an ESE binding SR proteins. Its 3′-part contains a decoy 5′-splice site (ss), which inhibits splicing at the bona fide 5′-ss. Only the 3D structure of a small NRS fragment had been experimentally studied. Here, by chemical and enzymatic probing, we determine the 2D structure of the entire RSV NRS. Structural analysis of other avian NRSs and comparison with all sequenced avian NRSs is in favour of a phylogenetic conservation of the NRS 2D structure. By combination of approaches: (i) in vitro and in cellulo splicing assays, (ii) footprinting assays and (iii) purification and analysis of reconstituted RNP complex, we define a small NRS element retaining splicing inhibitory property. We also demonstrate the capability of the SR protein 9G8 to increase NRS activity in vitro and in cellulo. Altogether these data bring new insights on how NRS fine tune splicing activity.
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Affiliation(s)
- Aileen Bar
- ARN, RNP, Structure-Fonction-maturation, Enzymologie Moléculaire et Structurale, Faculté des Sciences et Techniques, Nancy Université-UMR 7214 CNRS-UHP, BP 70239, 54506 Vandoeuvre-lès-Nancy cedex, France
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5
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Abstract
Over 40 different human immunodeficiency virus type 1 (HIV-1) mRNA species, both completely and incompletely spliced, are produced by alternative splicing of the primary viral RNA transcript. In addition, about half of the viral RNA remains unspliced and is transported to the cytoplasm where it is used both as mRNA and as genomic RNA. In general, the identities of the completely and incompletely spliced HIV-1 mRNA species are determined by the proximity of the open reading frames to the 5'-end of the mRNAs. The relative abundance of the mRNAs encoding the HIV-1 gene products is determined by the frequency of splicing at the different alternative 3'-splice sites. This chapter will highlight studies showing how HIV-1 uses exon definition to control the level of splicing at each of its 3'-splice sites through a combination of positively acting exonic splicing enhancer (ESE) elements, negatively acting exonic and intronic splicing silencer elements (ESS and ISS elements, respectively), and the 5'-splice sites of the regulated exons. Each of these splicing elements represent binding sites for cellular factors whose levels in the infected cell can determine the dominance of the positive or negative elements on HIV-1 alternative splicing. Both mutations of HIV-1 splicing elements and overexpression or inhibition of cellular splicing factors that bind to these elements have been used to show that disruption of regulated splicing inhibits HIV-1 replication. These studies have provided strong rationale for the investigation and development of antiviral drugs that specifically inhibit HIV-1 RNA splicing.
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6
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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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Kammler S, Otte M, Hauber I, Kjems J, Hauber J, Schaal H. The strength of the HIV-1 3' splice sites affects Rev function. Retrovirology 2006; 3:89. [PMID: 17144911 PMCID: PMC1697824 DOI: 10.1186/1742-4690-3-89] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2006] [Accepted: 12/04/2006] [Indexed: 11/16/2022] Open
Abstract
Background The HIV-1 Rev protein is a key component in the early to late switch in HIV-1 splicing from early intronless (e.g. tat, rev) to late intron-containing Rev-dependent (e.g. gag, vif, env) transcripts. Previous results suggested that cis-acting sequences and inefficient 5' and 3' splice sites are a prerequisite for Rev function. However, we and other groups have shown that two of the HIV-1 5' splice sites, D1 and D4, are efficiently used in vitro and in vivo. Here, we focus on the efficiency of the HIV-1 3' splice sites taking into consideration to what extent their intrinsic efficiencies are modulated by their downstream cis-acting exonic sequences. Furthermore, we delineate their role in RNA stabilization and Rev function. Results In the presence of an efficient upstream 5' splice site the integrity of the 3' splice site is not essential for Rev function whereas an efficient 3' splice site impairs Rev function. The detrimental effect of a strong 3' splice site on the amount of Rev-dependent intron-containing HIV-1 glycoprotein coding (env) mRNA is not compensatable by weakening the strength of the upstream 5' splice site. Swapping the HIV-1 3' splice sites in an RRE-containing minigene, we found a 3' splice site usage which was variably dependent on the presence of the usual downstream exonic sequence. The most evident activation of 3' splice site usage by its usual downstream exonic sequence was observed for 3' splice site A1 which was turned from an intrinsic very weak 3' splice site into the most active 3' splice site, even abolishing Rev activity. Performing pull-down experiments with nuclear extracts of HeLa cells we identified a novel ASF/SF2-dependent exonic splicing enhancer (ESE) within HIV-1 exon 2 consisting of a heptameric sequence motif occurring twice (M1 and M2) within this short non-coding leader exon. Single point mutation of M1 within an infectious molecular clone is detrimental for HIV-1 exon 2 recognition without affecting Rev-dependent vif expression. Conclusion Under the conditions of our assay, the rate limiting step of retroviral splicing, competing with Rev function, seems to be exclusively determined by the functional strength of the 3' splice site. The bipartite ASF/SF2-dependent ESE within HIV-1 exon 2 supports cross-talk between splice site pairs across exon 2 (exon definition) which is incompatible with processing of the intron-containing vif mRNA. We propose that Rev mediates a switch from exon to intron definition necessary for the expression of all intron-containing mRNAs.
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Affiliation(s)
- Susanne Kammler
- Institut für Virologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, Geb. 22.21, D-40225 Düsseldorf, Germany
- Department of Molecular Biology, University of Aarhus, C.F. Møllers Allé, Bldg. 1130, DK-8000 Aarhus C, Denmark
| | - Marianne Otte
- Institut für Virologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, Geb. 22.21, D-40225 Düsseldorf, Germany
- Institut für Genetik, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, Geb. 26.03, D-40225 Düsseldorf, Germany
| | - Ilona Hauber
- Heinrich-Pette-Institute for Experimental Virology and Immunology, Martinistrasse 52, D-20251 Hamburg, Germany
| | - Jørgen Kjems
- Department of Molecular Biology, University of Aarhus, C.F. Møllers Allé, Bldg. 1130, DK-8000 Aarhus C, Denmark
| | - Joachim Hauber
- Heinrich-Pette-Institute for Experimental Virology and Immunology, Martinistrasse 52, D-20251 Hamburg, Germany
| | - Heiner Schaal
- Institut für Virologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, Geb. 22.21, D-40225 Düsseldorf, Germany
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8
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Hallay H, Locker N, Ayadi L, Ropers D, Guittet E, Branlant C. Biochemical and NMR Study on the Competition between Proteins SC35, SRp40, and Heterogeneous Nuclear Ribonucleoprotein A1 at the HIV-1 Tat Exon 2 Splicing Site. J Biol Chem 2006; 281:37159-74. [PMID: 16990281 DOI: 10.1074/jbc.m603864200] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The human immunodeficiency virus, type 1, Tat protein plays a key role in virus multiplication. Because of its apoptotic property, its production is highly controlled. It depends upon the A3 splicing site utilization. A key control of site A3 activity is the ESS2 splicing silencer, which is located within the long stem-loop structure 3 (SLS3), far downstream from site A3. Here, by enzymatic footprints, we demonstrate the presence of several heterogeneous nuclear ribonucleoprotein (hnRNP) A1-binding sites on SLS3 and show the importance of the C-terminal Gly domain of hnRNP A1 in the formation of stable complexes containing several hnRNP A1 molecules bound on SLS3. Mutations in each of the UAG triplets in ESS2 strongly reduce the overall hnRNP A1 binding, showing the central role of ESS2 in hnRNP A1 assembly on SLS2-SLS3. Using NMR spectroscopy, we demonstrate the direct interaction of ESS2 with the RNA recognition motifs domains of hnRNP A1. This interaction has limited effect on the RNA two-dimensional structure. The SR proteins SC35 and SRp40 were found previously to be strong activators of site A3 utilization. By enzymatic and chemical footprints, we delineate their respective binding sites on SLS2 and SLS3 and find a strong similarity between the hnRNP A1-, SC35-, and SRp40-binding sites. The strongest SC35-binding site only has a modest contribution to site A3 activation. Hence, the main role of SR proteins at site A3 is to counteract hnRNP A1 binding on ESS2 and ESE2. Indeed, we found that ESE2 has inhibitory properties because of its ability to bind hnRNP A1.
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Affiliation(s)
- Houda Hallay
- UMR 7567 CNRS-Université Henri Poincaré-Nancy I, Boulevard des Aiguillettes, BP239, 54506 Vandoeuvre-lès-Nancy Cedex and Laboratoire de Chimie et Biologie Structurales, ICSN-CNRS, 1 Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
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9
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Jacquenet S, Decimo D, Muriaux D, Darlix JL. Dual effect of the SR proteins ASF/SF2, SC35 and 9G8 on HIV-1 RNA splicing and virion production. Retrovirology 2005; 2:33. [PMID: 15907217 PMCID: PMC1180853 DOI: 10.1186/1742-4690-2-33] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2005] [Accepted: 05/22/2005] [Indexed: 11/10/2022] Open
Abstract
In HIV-1 infected cells transcription of the integrated provirus generates the single full length 9 kb viral RNA, a major fraction of which is spliced to produce the single-spliced 4 kb RNAs and the multiple-spliced 2 kb RNAs. These spliced RNAs are the messengers for the Env glycoproteins and the viral regulatory factors. The cellular SR and hnRNP proteins were shown in vitro to control alternative splicing by binding cis-regulatory elements on the viral RNA. To better understand in vivo the role of the SR proteins on HIV-1 genomic RNA splicing and virion production, we used a human cell line expressing high levels of complete HIV-1 and either one of the ASF/SF2, SC35, and 9G8 SR proteins. Results show that over-expressing SR proteins caused a large reduction of genomic RNA and that each SR protein modified the viral 9 kb RNA splicing pattern in a specific mode. In fact, ASF/SF2 increased the level of Vpr RNA while SC35 and 9G8 caused a large increase in Tat RNA. As expected, overexpressing SR proteins caused a strong reduction of total Gag made. However, we observed by immuno-confocal microscopy an accumulation of Gag at the plasma membrane and in intracellular compartments while there is a dramatic reduction of Env protein made in most cells. Due to the negative impact of the SR proteins on the levels of genomic RNA and HIV-1 structural proteins much less virions were produced which retained part of their infectivity. In conclusion, SR proteins can down-regulate the late steps of HIV-1 replication.
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Affiliation(s)
- Sandrine Jacquenet
- Laboratoire de Médecine et Thérapeutique moléculaire, INSERM CIC9501, 15 rue du Bois de la Champelle, 54500 Vandoeuvre-lès-Nancy, France
- LaboRetro, Unité de Virologie Humaine, INSERM #412, Ecole Normale Supérieure de Lyon, IFR 128, 46 allée d'Italie, 69364 Lyon cedex 07, France
| | - Didier Decimo
- LaboRetro, Unité de Virologie Humaine, INSERM #412, Ecole Normale Supérieure de Lyon, IFR 128, 46 allée d'Italie, 69364 Lyon cedex 07, France
| | - Delphine Muriaux
- LaboRetro, Unité de Virologie Humaine, INSERM #412, Ecole Normale Supérieure de Lyon, IFR 128, 46 allée d'Italie, 69364 Lyon cedex 07, France
| | - Jean-Luc Darlix
- LaboRetro, Unité de Virologie Humaine, INSERM #412, Ecole Normale Supérieure de Lyon, IFR 128, 46 allée d'Italie, 69364 Lyon cedex 07, France
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10
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Ropers D, Ayadi L, Gattoni R, Jacquenet S, Damier L, Branlant C, Stévenin J. Differential effects of the SR proteins 9G8, SC35, ASF/SF2, and SRp40 on the utilization of the A1 to A5 splicing sites of HIV-1 RNA. J Biol Chem 2004; 279:29963-73. [PMID: 15123677 DOI: 10.1074/jbc.m404452200] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Splicing is a crucial step for human immunodeficiency virus, type 1 (HIV-1) multiplication; eight acceptor sites are used in competition to produce the vif, vpu, vpr, nef, env, tat, and rev mRNAs. The effects of SR proteins have only been investigated on a limited number of HIV-1 splicing sites by using small HIV-1 RNA pieces. To understand how SR proteins influence the use of HIV-1 splicing sites, we tested the effects of overproduction of individual SR proteins in HeLa cells on the splicing pattern of an HIV-1 RNA that contained all the splicing sites. The steady state levels of the HIV-1 mRNAs produced were quantified by reverse transcriptase-PCR. For interpretation of the data, transcripts containing one or several of the HIV-1 acceptor sites were spliced in vitro in the presence or the absence of one of the tested SR proteins. Both in vivo and in vitro, acceptor sites A2 and A3 were found to be strongly and specifically regulated by SR proteins. ASF/SF2 strongly activates site A2 and to a lesser extent site A1. As a result, upon ASF/SF2 overexpression, the vpr mRNA steady state level is specifically increased. SC35 and SRp40, but not 9G8, strongly activate site A3, and their overexpression ex vivo induces a dramatic accumulation of the tat mRNA, to the detriment of most of the other viral mRNAs. Here we showed by Western blot analysis that the Nef protein synthesis is strongly decreased by overexpression of SC35, SRp40, and ASF/SF2. Finally, activation by ASF/SF2 and 9G8 was found to be independent of the RS domain. This is the first investigation of the effects of variations of individual SR protein concentrations that is performed ex vivo on an RNA containing a complex set of splicing sites.
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Affiliation(s)
- Delphine Ropers
- Laboratoire de Maturation des ARN et Enzymologie Moléculaire, UMR CNRS 7567, Université Henri Poincaré Nancy 1, Boulevard des Aiguillettes, BP239, 54506 Vandoeuvre-lès-Nancy, France
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11
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Marchand V, Méreau A, Jacquenet S, Thomas D, Mougin A, Gattoni R, Stévenin J, Branlant C. A Janus splicing regulatory element modulates HIV-1 tat and rev mRNA production by coordination of hnRNP A1 cooperative binding. J Mol Biol 2002; 323:629-52. [PMID: 12419255 DOI: 10.1016/s0022-2836(02)00967-1] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Retroviral protein production depends upon alternative splicing of the viral transcript. The HIV-1 acceptor site A7 is required for tat and rev mRNA production. Production of the Tat transcriptional activator is highly controlled because of its apoptotic properties. Two silencer elements (ESS3 and ISS) and two enhancer elements (ESE2 and ESE3/(GAA)3) were previously identified at site A7. hnRNP A1 binds ISS and ESS3 and is involved in the inhibitory process, ASF/SF2 activates site A7 utilisation. Here, by using chemical and enzymatic probes we established the 2D structure of the HIV-1(BRU) RNA region containing site A7 and identified the RNA segments protected in nuclear extract and by purified hnRNP A1. ISS, ESE3/(GAA)3 and ESS3 are located in three distinct stem-loop structures (SLS1, 2 and 3). As expected, hnRNP A1 binds sites 1, 2 and 3 of ISS and ESS3b, and oligomerises on the polypurine sequence upstream of ESS3b. In addition, we discovered an unidentified hnRNP A1 binding site (AUAGAA), that overlaps ESE3/(GAA)3. On the basis of competition experiments, hnRNP A1 has a stronger affinity for this site than for ESS3b. By insertion of (GAA)3 alone or preceded by the AUA trinucleotide in a foreign context, the AUAGAA sequence was found to modulate strongly the (GAA)3 splicing enhancer activity. Cross-linking experiments on these heterologous RNAs and the SLS2-SLS3 HIV-1 RNA region, in nuclear extract and with recombinant proteins, showed that binding of hnRNP A1 to AUA(GAA)3 strongly competes the association of ASF/SF2 with (GAA)3. In addition, disruption of AUA(GAA)3 demonstrated a key role of this sequence in hnRNP A1 cooperative binding to the ISS and ESS3b inhibitors and hnRNP A1 oligomerisation on the polypurine sequence. Thus, depending on the cellular context ([ASF/SF2]/[hnRNP A1] ratio), AUA(GAA)3 will activate or repress site A7 utilisation and can thus be considered as a Janus splicing regulator.
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MESH Headings
- Alternative Splicing
- Base Sequence
- Binding Sites
- Electrophoretic Mobility Shift Assay
- Gene Expression Regulation, Viral
- Gene Products, rev/genetics
- Gene Products, tat/genetics
- HIV-1/genetics
- HeLa Cells
- Heterogeneous Nuclear Ribonucleoprotein A1
- Heterogeneous-Nuclear Ribonucleoprotein Group A-B/metabolism
- Humans
- Molecular Sequence Data
- Mutagenesis, Site-Directed
- Nucleic Acid Conformation
- Protein Binding
- RNA, Messenger/biosynthesis
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Viral/biosynthesis
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Silencer Elements, Transcriptional/genetics
- Transcription, Genetic
- rev Gene Products, Human Immunodeficiency Virus
- tat Gene Products, Human Immunodeficiency Virus
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Affiliation(s)
- Virginie Marchand
- Laboratoire de Maturation des ARN et Enzymologie Moléculaire, UMR 7567 UHP-CNRS, Université Henri Poincaré Nancy 1, Boulevard des Aiguillettes, BP239, 54506 Cedex, Vandoeuvre-lès-Nancy, France
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12
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Jacquenet S, Méreau A, Bilodeau PS, Damier L, Stoltzfus CM, Branlant C. A second exon splicing silencer within human immunodeficiency virus type 1 tat exon 2 represses splicing of Tat mRNA and binds protein hnRNP H. J Biol Chem 2001; 276:40464-75. [PMID: 11526107 DOI: 10.1074/jbc.m104070200] [Citation(s) in RCA: 112] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
An equilibrium between spliced and unspliced primary transcripts is essential for retrovirus multiplication. This equilibrium is maintained by the presence of inefficient splice sites. The A3 3'-splice site of human immunodeficiency virus type I (HIV-1) is required for Tat mRNA production. The infrequent utilization of this splice site has been attributed to the presence of a suboptimal polypyrimidine tract and an exonic splicing silencer (ESS2) in tat exon 2 approximately 60 nucleotides downstream of 3'-splice site A3. Here, using site-directed mutagenesis followed by analysis of splicing in vitro and in HeLa cells, we show that the 5' extremity of tat exon 2 contains a second exonic splicing silencer (ESS2p), which acts to repress splice site A3. The inhibitory property of this exonic silencer was active when inserted downstream of another HIV-1 3'-splice site (A2). Protein hnRNP H binds to this inhibitory element, and two U-to-C substitutions within the ESS2p element cause a decreased hnRNP H affinity with a concomitant increase in splicing efficiency at 3'-splice site A3. This suggests that hnRNP H is directly involved in splicing inhibition. We propose that hnRNP H binds to the HIV-1 ESS2p element and competes with U2AF(35) for binding to the exon sequence flanking 3'-splice site A3. This binding results in the inhibition of splicing at 3'-splice site A3.
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Affiliation(s)
- S Jacquenet
- Laboratoire de Maturation des Acide Ribo-Nucléotidique et Enzymologie Moléculaire, Unité Mixte de Recherche 7567 Université Henri Poincarré-CNRS, Boulevard des Aiguillettes, BP239, 54506 Vandoeuvre-lès-Nancy cedex, France
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13
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Bilodeau PS, Domsic JK, Mayeda A, Krainer AR, Stoltzfus CM. RNA splicing at human immunodeficiency virus type 1 3' splice site A2 is regulated by binding of hnRNP A/B proteins to an exonic splicing silencer element. J Virol 2001; 75:8487-97. [PMID: 11507194 PMCID: PMC115094 DOI: 10.1128/jvi.75.18.8487-8497.2001] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The synthesis of human immunodeficiency virus type 1 (HIV-1) mRNAs is a complex process by which more than 30 different mRNA species are produced by alternative splicing of a single primary RNA transcript. HIV-1 splice sites are used with significantly different efficiencies, resulting in different levels of mRNA species in infected cells. Splicing of Tat mRNA, which is present at relatively low levels in infected cells, is repressed by the presence of exonic splicing silencers (ESS) within the two tat coding exons (ESS2 and ESS3). These ESS elements contain the consensus sequence PyUAG. Here we show that the efficiency of splicing at 3' splice site A2, which is used to generate Vpr mRNA, is also regulated by the presence of an ESS (ESSV), which has sequence homology to ESS2 and ESS3. Mutagenesis of the three PyUAG motifs within ESSV increases splicing at splice site A2, resulting in increased Vpr mRNA levels and reduced skipping of the noncoding exon flanked by A2 and D3. The increase in Vpr mRNA levels and the reduced skipping also occur when splice site D3 is mutated toward the consensus sequence. By in vitro splicing assays, we show that ESSV represses splicing when placed downstream of a heterologous splice site. A1, A1(B), A2, and B1 hnRNPs preferentially bind to ESSV RNA compared to ESSV mutant RNA. Each of these proteins, when added back to HeLa cell nuclear extracts depleted of ESSV-binding factors, is able to restore splicing repression. The results suggest that coordinate repression of HIV-1 RNA splicing is mediated by members of the hnRNP A/B protein family.
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Affiliation(s)
- P S Bilodeau
- Department of Microbiology, University of Iowa, Iowa City, Iowa 52242, USA
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14
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Jacquenet S, Ropers D, Bilodeau PS, Damier L, Mougin A, Stoltzfus CM, Branlant C. Conserved stem-loop structures in the HIV-1 RNA region containing the A3 3' splice site and its cis-regulatory element: possible involvement in RNA splicing. Nucleic Acids Res 2001; 29:464-78. [PMID: 11139617 PMCID: PMC29680 DOI: 10.1093/nar/29.2.464] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The HIV-1 transcript is alternatively spliced to over 30 different mRNAs. Whether RNA secondary structure can influence HIV-1 RNA alternative splicing has not previously been examined. Here we have determined the secondary structure of the HIV-1/BRU RNA segment, containing the alternative A3, A4a, A4b, A4c and A5 3' splice sites. Site A3, required for tat mRNA production, is contained in the terminal loop of a stem-loop structure (SLS2), which is highly conserved in HIV-1 and related SIVcpz strains. The exon splicing silencer (ESS2) acting on site A3 is located in a long irregular stem-loop structure (SLS3). Two SLS3 domains were protected by nuclear components under splicing condition assays. One contains the A4c branch points and a putative SR protein binding site. The other one is adjacent to ESS2. Unexpectedly, only the 3' A residue of ESS2 was protected. The suboptimal A3 polypyrimidine tract (PPT) is base paired. Using site-directed mutagenesis and transfection of a mini-HIV-1 cDNA into HeLa cells, we found that, in a wild-type PPT context, a mutation of the A3 downstream sequence that reinforced SLS2 stability decreased site A3 utilization. This was not the case with an optimized PPT. Hence, sequence and secondary structure of the PPT may cooperate in limiting site A3 utilization.
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Affiliation(s)
- S Jacquenet
- Laboratoire de Maturation des ARN et Enzymologie Moléculaire, UMR 7567 UHP-CNRS, France
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15
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Bourara K, Litvak S, Araya A. Generation of G-to-A and C-to-U changes in HIV-1 transcripts by RNA editing. Science 2000; 289:1564-6. [PMID: 10968794 DOI: 10.1126/science.289.5484.1564] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
RNA editing involves posttranscriptional alterations of messenger RNA (mRNA) sequences modifying the information content encoded by the genetic message. Here, it is shown that, in chronically infected H9 cells, human immunodeficiency virus-type 1 (HIV-1) mRNAs undergo guanine-to-adenine (G-to-A) and cytosine-to-uracil (C-to-U) changes. G-to-A modification in the untranslated region of exon 1 was present only in spliced HIV-1 mRNAs. The creation of stop codons in HIV-1 mRNAs may function to control the translation of viral proteins, such as viral protein R, that are involved in the regulation of HIV-1 expression and the survival of chronically infected cells.
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Affiliation(s)
- K Bourara
- Laboratoire de Réplication et Expression des Génomes Eucaryotes et Rétroviraux, UMR 5097, CNRS-Université Victor Segalen-Bordeaux 2, France
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16
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Swanson AK, Stoltzfus CM. Overlapping cis sites used for splicing of HIV-1 env/nef and rev mRNAs. J Biol Chem 1998; 273:34551-7. [PMID: 9852125 DOI: 10.1074/jbc.273.51.34551] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Alternative splicing is used to generate more than 30 human immunodeficiency virus type 1 (HIV-1) spliced and unspliced mRNAs from a single primary transcript. The abundance of HIV-1 mRNAs is determined by the efficiencies with which its different 5' and 3' splice sites are used. Three splice sites (A4c, A4a, and A4b) are upstream of the rev initiator AUG. RNAs spliced at A4c, A4a, and A4b are used as mRNAs for Rev. Another 3' splice site (A5) is immediately downstream of the rev initiator. RNAs spliced at A5 are used as mRNAs for Env and Nef. In this report, primer extension analysis of splicing intermediates was used to show that there are eight branch points in this region, all of which map to adenosine residues. In addition, cis elements recognized by the cellular splicing machinery overlap; the two most 3' branch points overlap with the AG dinucleotides at rev 3' splice sites A4a and A4b. Competition of the overlapping cis sites for different splicing factors may play a role in maintaining the appropriate balance of mRNAs in HIV-1-infected cells. In support of this possibility, mutations at rev 3' splice site A4b AG dinucleotide dramatically increased splicing of the env/nef 3' splice site A5. This correlated with increased usage of the four most 3' branch points, which include those within the rev 3' splice site AG dinucleotides. Consistent with these results, analysis of a mutant in which three of the four env/nef branch points were inactivated indicated that use of splice site A5 was inhibited and splicing was shifted predominantly to the most 5' rev 3' splice site A4c with preferential use of the two most 5' branch points. Our results suggest that spliceosomes formed at rev A4a-4b, rev A4c, and env/nef A5 3' splice sites each recognize different subsets of the eight branch point sequences.
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Affiliation(s)
- A K Swanson
- Department of Microbiology and Program in Molecular Biology, University of Iowa, Iowa City, Iowa 52242, USA
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17
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Si ZH, Rauch D, Stoltzfus CM. The exon splicing silencer in human immunodeficiency virus type 1 Tat exon 3 is bipartite and acts early in spliceosome assembly. Mol Cell Biol 1998; 18:5404-13. [PMID: 9710624 PMCID: PMC109125 DOI: 10.1128/mcb.18.9.5404] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/1998] [Accepted: 06/08/1998] [Indexed: 11/20/2022] Open
Abstract
Inefficient splicing of human immunodeficiency virus type 1 (HIV-1) RNA is necessary to preserve unspliced and singly spliced viral RNAs for transport to the cytoplasm by the Rev-dependent pathway. Signals within the HIV-1 genome that control the rate of splicing include weak 3' splice sites, exon splicing enhancers (ESE), and exon splicing silencers (ESS). We have previously shown that an ESS present within tat exon 2 (ESS2) and a suboptimal 3' splice site together act to inhibit splicing at the 3' splice site flanking tat exon 2. This occurs at an early step in spliceosome assembly. Splicing at the 3' splice site flanking tat exon 3 is regulated by a bipartite element composed of an ESE and an ESS (ESS3). Here we show that ESS3 is composed of two smaller elements (AGAUCC and UUAG) that can inhibit splicing independently. We also show that ESS3 is more active in the context of a heterologous suboptimal splice site than of an optimal 3' splice site. ESS3 inhibits splicing by blocking the formation of a functional spliceosome at an early step, since A complexes are not detected in the presence of ESS3. Competitor RNAs containing either ESS2 or ESS3 relieve inhibition of splicing of substrates containing ESS3 or ESS2. This suggests that a common cellular factor(s) may be required for the inhibition of tat mRNA splicing mediated by ESS2 and ESS3.
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MESH Headings
- Base Sequence
- Cloning, Organism
- Exons
- Gene Products, tat/biosynthesis
- Genes, tat
- HIV Enhancer
- HIV-1/genetics
- Humans
- Kinetics
- Mutagenesis, Site-Directed
- RNA Splicing
- RNA, Messenger/chemistry
- RNA, Messenger/metabolism
- RNA, Viral/chemistry
- RNA, Viral/metabolism
- Regulatory Sequences, Nucleic Acid
- Spliceosomes/physiology
- tat Gene Products, Human Immunodeficiency Virus
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Affiliation(s)
- Z H Si
- Department of Microbiology, University of Iowa, Iowa City, Iowa 52242, USA
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