1
|
Zarudnaya MI, Potyahaylo AL, Kolomiets IM, Gorb LG. Structural diversity of the region encompassing DIS, SD and Psi hairpins in HIV and SIV genomes. Virus Res 2023; 336:199197. [PMID: 37574135 PMCID: PMC10483063 DOI: 10.1016/j.virusres.2023.199197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/15/2023]
Abstract
We investigated in silico the secondary structure of the region encompassing DIS, SD and Psi hairpins in HIV-1 genomes of rare groups N, O and P, HIV-2 genomes and SIV genomes from chimpanzees, gorillas and monkeys. We found that the structure of this region in SIVcpzptt genomes of the 1st and the 2nd clusters is similar to that in HIV-1 genomes of groups M and N, respectively. Further, the structure of the region encompassing DIS, SD and Psi hairpins is similar in HIV-1 genomes of groups O and P and SIVgor genomes. Here we report that the DIS hairpin and truncated Psi hairpin are conserved in all HIV-1 and SIVcpz/gor genomes studied, while only the sequence of the splice donor site, but not the architecture of the SD hairpin involving this signal is conserved in HIV-1N/O/P and SIVcpz/gor genomes. A study on the 5' leader structure in genomes of 28 different SIV lineages infecting monkeys showed that the domain closed by U5-AUG duplex can form in all these genomes. This domain mainly consists of 2 subdomains, one of which includes the signal PBS (PBS subdomain) and another contains a putative DIS hairpin (DIS subdomain). DIS subdomains contain 1-8 hairpins. None of them is similar to those in HIV-1 or SIVcpz/gor genomes. The palindrome GUGCAC was found only in SIVdrl/mnd-2, the GACGC-GCGUC duplex (Sakuragi et al., 2012) - only in SIVrcm/drl/mnd-2 and a putative 5' G-quadruplex - in SIVdeb/drl/rcm/stm genomes. In genomes of eight SIV lineages, DIS hairpin has palindrome UGCGCA. Studies on the 5' leader in 64 HIV-2 genomes of different subtypes showed, in particular, that this region has sequences of a putative 5' G-quadruplex and a putative duplex similar to the GACGC-GCGUC duplex. The secondary structures of the region encompassing DIS, SD and Psi hairpins in HIV-2 genomes of subtype B and recombinant 01_AB are similar and differ from that in genomes of subtype A.
Collapse
Affiliation(s)
- M I Zarudnaya
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv, 03143, Ukraine
| | - A L Potyahaylo
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv, 03143, Ukraine
| | - I M Kolomiets
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv, 03143, Ukraine
| | - L G Gorb
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv, 03143, Ukraine.
| |
Collapse
|
2
|
Li D, Yu W, Lai M. Towards understandings of serine/arginine-rich splicing factors. Acta Pharm Sin B 2023; 13:3181-3207. [PMID: 37655328 PMCID: PMC10465970 DOI: 10.1016/j.apsb.2023.05.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/13/2023] [Accepted: 05/06/2023] [Indexed: 09/02/2023] Open
Abstract
Serine/arginine-rich splicing factors (SRSFs) refer to twelve RNA-binding proteins which regulate splice site recognition and spliceosome assembly during precursor messenger RNA splicing. SRSFs also participate in other RNA metabolic events, such as transcription, translation and nonsense-mediated decay, during their shuttling between nucleus and cytoplasm, making them indispensable for genome diversity and cellular activity. Of note, aberrant SRSF expression and/or mutations elicit fallacies in gene splicing, leading to the generation of pathogenic gene and protein isoforms, which highlights the therapeutic potential of targeting SRSF to treat diseases. In this review, we updated current understanding of SRSF structures and functions in RNA metabolism. Next, we analyzed SRSF-induced aberrant gene expression and their pathogenic outcomes in cancers and non-tumor diseases. The development of some well-characterized SRSF inhibitors was discussed in detail. We hope this review will contribute to future studies of SRSF functions and drug development targeting SRSFs.
Collapse
Affiliation(s)
- Dianyang Li
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Wenying Yu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Maode Lai
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China
- Department of Pathology, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Science (2019RU042), Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou 310058, China
| |
Collapse
|
3
|
Zarudnaya MI, Potyahaylo AL, Kolomiets IM, Gorb LG. Genome sequence analysis suggests coevolution of the DIS, SD, and Psi hairpins in HIV-1 genomes. Virus Res 2022; 321:198910. [PMID: 36070810 DOI: 10.1016/j.virusres.2022.198910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/28/2022] [Accepted: 08/31/2022] [Indexed: 12/24/2022]
Abstract
HIV-1 RNA dimerization is a critical step in viral life cycle. It is a prerequisite for genome packaging and plays an important role in reverse transcription and recombination. Dimerization is promoted by the DIS (dimerization initiation site) hairpin located in the 5' leader of HIV-1 genome. Despite the high genetic diversity in HIV-1 group M, only five apical loops (AAGCGCGCA, AAGUGCGCA, AAGUGCACA, AGGUGCACA and AGUGCAC) are commonly found in DIS hairpins. We refer to the parent DISes with these apical loops as DISLai, DISTrans, DISF, DISMal, and DISC, respectively. Based on identity or similarity of DIS hairpins to parent DISes, we distributed HIV-1 M genomes into five dimerization groups. Comparison of the primary and secondary structures of DIS, SD and Psi hairpins in about 3000 HIV-1 M genomes showed that the mutation frequencies at particular nucleotide positions of these hairpins differ among the dimerization groups, and DISF may be an origin of other parent DISes. We found that DIS, SD and Psi hairpins have hundreds of variants, only some of them occurring rather frequently. The lower part of DIS hairpin with G x AGG internal loop is highly conserved in both HIV-1 and SIV genomes. We supposed that the G-quadruplex, located 56 nts downstream of the Gag start codon, may participate in switching of HIV-1 leader RNA from BMH (branched multiple hairpins) to LDI (long distance interaction) conformation.
Collapse
Affiliation(s)
- Margarita I Zarudnaya
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Akademika Zabolotnoho Str, Kyiv 03143, Ukraine
| | - Andriy L Potyahaylo
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Akademika Zabolotnoho Str, Kyiv 03143, Ukraine
| | - Iryna M Kolomiets
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Akademika Zabolotnoho Str, Kyiv 03143, Ukraine
| | - Leonid G Gorb
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Akademika Zabolotnoho Str, Kyiv 03143, Ukraine.
| |
Collapse
|
4
|
Dahal S, Clayton K, Been T, Fernet-Brochu R, Ocando AV, Balachandran A, Poirier M, Maldonado RK, Shkreta L, Boligan KF, Guvenc F, Rahman F, Branch D, Bell B, Chabot B, Gray-Owen SD, Parent LJ, Cochrane A. Opposing roles of CLK SR kinases in controlling HIV-1 gene expression and latency. Retrovirology 2022; 19:18. [PMID: 35986377 PMCID: PMC9389714 DOI: 10.1186/s12977-022-00605-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 07/29/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The generation of over 69 spliced HIV-1 mRNAs from one primary transcript by alternative RNA splicing emphasizes the central role that RNA processing plays in HIV-1 replication. Control is mediated in part through the action of host SR proteins whose activity is regulated by multiple SR kinases (CLK1-4, SRPKs). METHODS Both shRNA depletion and small molecule inhibitors of host SR kinases were used in T cell lines and primary cells to evaluate the role of these factors in the regulation of HIV-1 gene expression. Effects on virus expression were assessed using western blotting, RT-qPCR, and immunofluorescence. RESULTS The studies demonstrate that SR kinases play distinct roles; depletion of CLK1 enhanced HIV-1 gene expression, reduction of CLK2 or SRPK1 suppressed it, whereas CLK3 depletion had a modest impact. The opposing effects of CLK1 vs. CLK2 depletion were due to action at distinct steps; reduction of CLK1 increased HIV-1 promoter activity while depletion of CLK2 affected steps after transcript initiation. Reduced CLK1 expression also enhanced the response to several latency reversing agents, in part, by increasing the frequency of responding cells, consistent with a role in regulating provirus latency. To determine whether small molecule modulation of SR kinase function could be used to control HIV-1 replication, we screened a GSK library of protein kinase inhibitors (PKIS) and identified several pyrazolo[1,5-b] pyridazine derivatives that suppress HIV-1 gene expression/replication with an EC50 ~ 50 nM. The compounds suppressed HIV-1 protein and viral RNA accumulation with minimal impact on cell viability, inhibiting CLK1 and CLK2 but not CLK3 function, thereby selectively altering the abundance of individual CLK and SR proteins in cells. CONCLUSIONS These findings demonstrate the unique roles played by individual SR kinases in regulating HIV-1 gene expression, validating the targeting of these functions to either enhance latency reversal, essential for "Kick-and-Kill" strategies, or to silence HIV protein expression for "Block-and-Lock" strategies.
Collapse
Affiliation(s)
- Subha Dahal
- grid.17063.330000 0001 2157 2938Dept. of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S1A8 Canada
| | - Kiera Clayton
- grid.168645.80000 0001 0742 0364Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Terek Been
- grid.17063.330000 0001 2157 2938Dept. of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S1A8 Canada
| | - Raphaële Fernet-Brochu
- grid.17063.330000 0001 2157 2938Dept. of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S1A8 Canada
| | - Alonso Villasmil Ocando
- grid.461656.60000 0004 0489 3491Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139 USA
| | - Ahalya Balachandran
- grid.17063.330000 0001 2157 2938Dept. of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S1A8 Canada
| | - Mikaël Poirier
- grid.86715.3d0000 0000 9064 6198Dept. of Microbiology & Infectious Diseases, Université de Sherbrooke, Sherbrooke, QC Canada
| | - Rebecca Kaddis Maldonado
- grid.240473.60000 0004 0543 9901Department of Medicine, Penn State College of Medicine, Hershey, PA 17033 USA ,grid.240473.60000 0004 0543 9901Microbiology & Immunology, Penn State College of Medicine, Hershey, PA 17033 USA
| | - Lulzim Shkreta
- grid.86715.3d0000 0000 9064 6198Dept. of Microbiology & Infectious Diseases, Université de Sherbrooke, Sherbrooke, QC Canada
| | - Kayluz Frias Boligan
- grid.423370.10000 0001 0285 1288Center for Innovation, Canadian Blood Services, Toronto, ON Canada
| | - Furkan Guvenc
- grid.17063.330000 0001 2157 2938Dept. of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S1A8 Canada
| | - Fariha Rahman
- grid.17063.330000 0001 2157 2938Dept. of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S1A8 Canada
| | - Donald Branch
- grid.423370.10000 0001 0285 1288Center for Innovation, Canadian Blood Services, Toronto, ON Canada
| | - Brendan Bell
- grid.86715.3d0000 0000 9064 6198Dept. of Microbiology & Infectious Diseases, Université de Sherbrooke, Sherbrooke, QC Canada
| | - Benoit Chabot
- grid.86715.3d0000 0000 9064 6198Dept. of Microbiology & Infectious Diseases, Université de Sherbrooke, Sherbrooke, QC Canada
| | - Scott D. Gray-Owen
- grid.17063.330000 0001 2157 2938Dept. of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S1A8 Canada
| | - Leslie J. Parent
- grid.240473.60000 0004 0543 9901Department of Medicine, Penn State College of Medicine, Hershey, PA 17033 USA ,grid.240473.60000 0004 0543 9901Microbiology & Immunology, Penn State College of Medicine, Hershey, PA 17033 USA
| | - Alan Cochrane
- grid.17063.330000 0001 2157 2938Dept. of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON M5S1A8 Canada
| |
Collapse
|
5
|
Transcriptional behavior of the HIV-1 promoter in context of the BACH2 prominent proviral integration gene. Virus Res 2020; 293:198260. [PMID: 33316352 DOI: 10.1016/j.virusres.2020.198260] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 12/04/2020] [Indexed: 11/23/2022]
Abstract
Chronic infection with human immunodeficiency virus (HIV)-1 is characterized by accumulation of proviral sequences in the genome of target cells. Integration of viral DNA in patients on long-term antiretroviral therapy selectively persists at preferential loci, suggesting site-specific crosstalk of viral sequences and human genes. This crosstalk likely contributes to chronic HIV disease through modulation of host immune pathways and emergence of clonal infected cell populations. To systematically interrogate such effects, we undertook genome engineering to generate Jurkat cell models that replicate integration of HIV-1 long terminal repeat (LTR) sequences at the BTB and CNC Homolog 2 (BACH2) integration locus. This locus is a prominent HIV-1 integration gene in chronic infection, found in 30 % of long-term treated patients with mapped proviral integrations. Using five clonal models carrying an LTR-driven reporter at different BACH2 intergenic regions, we here show that LTR transcriptional activity is repressed in BACH2 regions associated with proviral-DNA integrations in vivo but not in a control region. Our data indicates that this repression is in part epigenetically regulated, particularly through DNA methylation. Importantly, we demonstrate that transcriptional activity of the LTR is independent of BACH2 gene transcription and vice versa in our models. This suggests no transcriptional interference of endogenous and HIV-1 promoters. Taken together, our study provides first insights into how activity of HIV-1 LTR sequences is regulated at the BACH2 locus as prominent example for a recurrently-detected integration gene in chronic infection. Given the importance of integration-site dependent virus/host crosstalk for chronic HIV disease, our findings for the BACH2 locus have potential implications for future therapeutic strategies.
Collapse
|
6
|
Nguyen Quang N, Goudey S, Ségéral E, Mohammad A, Lemoine S, Blugeon C, Versapuech M, Paillart JC, Berlioz-Torrent C, Emiliani S, Gallois-Montbrun S. Dynamic nanopore long-read sequencing analysis of HIV-1 splicing events during the early steps of infection. Retrovirology 2020; 17:25. [PMID: 32807178 PMCID: PMC7433067 DOI: 10.1186/s12977-020-00533-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/07/2020] [Indexed: 12/14/2022] Open
Abstract
Background Alternative splicing is a key step in Human Immunodeficiency Virus type 1 (HIV-1) replication that is tightly regulated both temporally and spatially. More than 50 different transcripts can be generated from a single HIV-1 unspliced pre-messenger RNA (pre-mRNA) and a balanced proportion of unspliced and spliced transcripts is critical for the production of infectious virions. Understanding the mechanisms involved in the regulation of viral RNA is therefore of potential therapeutic interest. However, monitoring the regulation of alternative splicing events at a transcriptome-wide level during cell infection is challenging. Here we used the long-read cDNA sequencing developed by Oxford Nanopore Technologies (ONT) to explore in a quantitative manner the complexity of the HIV-1 transcriptome regulation in infected primary CD4+ T cells. Results ONT reads mapping to the viral genome proved sufficiently long to span all possible splice junctions, even distant ones, and to be assigned to a total of 150 exon combinations. Fifty-three viral RNA isoforms, including 14 new ones were further considered for quantification. Relative levels of viral RNAs determined by ONT sequencing showed a high degree of reproducibility, compared favourably to those produced in previous reports and highly correlated with quantitative PCR (qPCR) data. To get further insights into alternative splicing regulation, we then compiled quantifications of splice site (SS) usage and transcript levels to build “splice trees”, a quantitative representation of the cascade of events leading to the different viral isoforms. This approach allowed visualizing the complete rewiring of SS usages upon perturbation of SS D2 and its impact on viral isoform levels. Furthermore, we produced the first dynamic picture of the cascade of events occurring between 12 and 24 h of viral infection. In particular, our data highlighted the importance of non-coding exons in viral RNA transcriptome regulation. Conclusion ONT sequencing is a convenient and reliable strategy that enabled us to grasp the dynamic of the early splicing events modulating the viral RNA landscape in HIV-1 infected cells.
Collapse
Affiliation(s)
- Nam Nguyen Quang
- Institut Cochin, INSERM, CNRS, Université de Paris, 75014, Paris, France
| | - Sophie Goudey
- Institut Cochin, INSERM, CNRS, Université de Paris, 75014, Paris, France
| | - Emmanuel Ségéral
- Institut Cochin, INSERM, CNRS, Université de Paris, 75014, Paris, France
| | - Ammara Mohammad
- Genomic Facility, Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Sophie Lemoine
- Genomic Facility, Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Corinne Blugeon
- Genomic Facility, Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Margaux Versapuech
- Institut Cochin, INSERM, CNRS, Université de Paris, 75014, Paris, France
| | - Jean-Christophe Paillart
- CNRS, Architecture et Réactivité de l'ARN, UPR 9002, IBMC, Université de Strasbourg, Strasbourg, France
| | | | - Stéphane Emiliani
- Institut Cochin, INSERM, CNRS, Université de Paris, 75014, Paris, France.
| | | |
Collapse
|
7
|
Disruption by SaCas9 Endonuclease of HERV-K env, a Retroviral Gene with Oncogenic and Neuropathogenic Potential, Inhibits Molecules Involved in Cancer and Amyotrophic Lateral Sclerosis. Viruses 2018; 10:v10080412. [PMID: 30087231 PMCID: PMC6115762 DOI: 10.3390/v10080412] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/03/2018] [Accepted: 08/04/2018] [Indexed: 12/14/2022] Open
Abstract
The human endogenous retrovirus (HERV)-K, human mouse mammary tumor virus like-2 (HML-2) subgroup of HERVs is activated in several tumors and has been related to prostate cancer progression and motor neuron diseases. The cellular splicing factor 2/alternative splicing factor (SF2/ASF) is a positive regulator of gene expression, coded by a potent proto-oncogene, amplified, and abnormally expressed in tumors. TAR DNA-binding protein-43 (TDP-43) is a DNA/RNA-binding protein, negative regulator of alternative splicing, known for causing neurodegeneration, and with complex roles in oncogenesis. We used the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology, with the Cas9 system from Staphylococcus aureus (SaCas9), to disrupt the HERV-K(HML-2)env gene, and evaluated the effects on cultured cells. The tool was tested on human prostate cancer LNCaP cells, whose HERV-Kenv transcription profile is known. It caused HERV-K(HML-2)env disruption (the first reported of a HERV gene), as evaluated by DNA sequencing, and inhibition of env transcripts and proteins. The HERV-K(HML-2)env disruption was found to interfere with important regulators of cell expression and proliferation, involved in manaling, RNA-binding, and alternative splicing, such as epidermal growth factor receptor (EGF-R), nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), SF2/ASF, and TDP-43. These novel findings suggest that HERV-K is not an innocent bystander, they reinforce its links to oncogenesis and motor neuron diseases, and they open potential innovative therapeutic options.
Collapse
|
8
|
Wiredja DD, Tabler CO, Schlatzer DM, Li M, Chance MR, Tilton JC. Global phosphoproteomics of CCR5-tropic HIV-1 signaling reveals reprogramming of cellular protein production pathways and identifies p70-S6K1 and MK2 as HIV-responsive kinases required for optimal infection of CD4+ T cells. Retrovirology 2018; 15:44. [PMID: 29970186 PMCID: PMC6029029 DOI: 10.1186/s12977-018-0423-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 05/26/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Viral reprogramming of host cells enhances replication and is initiated by viral interaction with the cell surface. Upon human immunodeficiency virus (HIV) binding to CD4+ T cells, a signal transduction cascade is initiated that reorganizes the actin cytoskeleton, activates transcription factors, and alters mRNA splicing pathways. METHODS We used a quantitative mass spectrometry-based phosphoproteomic approach to investigate signal transduction cascades initiated by CCR5-tropic HIV, which accounts for virtually all transmitted viruses and the vast majority of viruses worldwide. RESULTS CCR5-HIV signaling induced significant reprogramming of the actin cytoskeleton and mRNA splicing pathways, as previously described. In addition, CCR5-HIV signaling induced profound changes to the mRNA transcription, processing, translation, and post-translational modifications pathways, indicating that virtually every stage of protein production is affected. Furthermore, we identified two kinases regulated by CCR5-HIV signaling-p70-S6K1 (RPS6KB1) and MK2 (MAPKAPK2)-that were also required for optimal HIV infection of CD4+ T cells. These kinases regulate protein translation and cytoskeletal architecture, respectively, reinforcing the importance of these pathways in viral replication. Additionally, we found that blockade of CCR5 signaling by maraviroc had relatively modest effects on CCR5-HIV signaling, in agreement with reports that signaling by CCR5 is dispensable for HIV infection but in contrast to the critical effects of CXCR4 on cortical actin reorganization. CONCLUSIONS These results demonstrate that CCR5-tropic HIV induces significant reprogramming of host CD4+ T cell protein production pathways and identifies two novel kinases induced upon viral binding to the cell surface that are critical for HIV replication in host cells.
Collapse
Affiliation(s)
- Danica D Wiredja
- Department of Nutrition, Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Caroline O Tabler
- Department of Nutrition, Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Daniela M Schlatzer
- Department of Nutrition, Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Ming Li
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Mark R Chance
- Department of Nutrition, Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - John C Tilton
- Department of Nutrition, Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.
| |
Collapse
|
9
|
The HIV-1 Tat Protein Enhances Splicing at the Major Splice Donor Site. J Virol 2018; 92:JVI.01855-17. [PMID: 29743356 DOI: 10.1128/jvi.01855-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 04/25/2018] [Indexed: 12/23/2022] Open
Abstract
Transcription of the HIV-1 proviral DNA and subsequent processing of the primary transcript results in the production of a large set of unspliced and differentially spliced viral RNAs. The major splice donor site (5'ss) that is located in the untranslated leader of the HIV-1 transcript is used for the production of all spliced RNAs, and splicing at this site has to be tightly regulated to allow the balanced production of all viral RNAs and proteins. We demonstrate that the viral Tat protein, which is known to activate viral transcription, also stimulates splicing at the major 5'ss. As for the transcription effect, Tat requires the viral long terminal repeat promoter and the trans-acting responsive RNA hairpin for splicing regulation. These results indicate that HIV-1 transcription and splicing are tightly coupled processes through the coordinated action of the essential Tat protein.IMPORTANCE The HIV-1 proviral DNA encodes a single RNA transcript that is used as RNA genome and packaged into newly assembled virus particles. This full-length RNA is also used as mRNA for the production of structural and enzymatic proteins. Production of other essential viral proteins depends on alternative splicing of the primary transcript, which yields a large set of differentially spliced mRNAs. Optimal virus replication requires a balanced production of all viral RNAs, which means that the splicing process has to be strictly regulated. We show that the HIV-1 Tat protein, a factor that is well known for its transcription activating function, also stimulates splicing. Thus, Tat controls not only the level of the viral RNA but also the balance between spliced and unspliced RNAs.
Collapse
|
10
|
Smyth RP, Smith MR, Jousset AC, Despons L, Laumond G, Decoville T, Cattenoz P, Moog C, Jossinet F, Mougel M, Paillart JC, von Kleist M, Marquet R. In cell mutational interference mapping experiment (in cell MIME) identifies the 5' polyadenylation signal as a dual regulator of HIV-1 genomic RNA production and packaging. Nucleic Acids Res 2018; 46:e57. [PMID: 29514260 PMCID: PMC5961354 DOI: 10.1093/nar/gky152] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/02/2018] [Accepted: 03/01/2018] [Indexed: 12/28/2022] Open
Abstract
Non-coding RNA regulatory elements are important for viral replication, making them promising targets for therapeutic intervention. However, regulatory RNA is challenging to detect and characterise using classical structure-function assays. Here, we present in cell Mutational Interference Mapping Experiment (in cell MIME) as a way to define RNA regulatory landscapes at single nucleotide resolution under native conditions. In cell MIME is based on (i) random mutation of an RNA target, (ii) expression of mutated RNA in cells, (iii) physical separation of RNA into functional and non-functional populations, and (iv) high-throughput sequencing to identify mutations affecting function. We used in cell MIME to define RNA elements within the 5' region of the HIV-1 genomic RNA (gRNA) that are important for viral replication in cells. We identified three distinct RNA motifs controlling intracellular gRNA production, and two distinct motifs required for gRNA packaging into virions. Our analysis reveals the 73AAUAAA78 polyadenylation motif within the 5' PolyA domain as a dual regulator of gRNA production and gRNA packaging, and demonstrates that a functional polyadenylation signal is required for viral packaging even though it negatively affects gRNA production.
Collapse
Affiliation(s)
- Redmond P Smyth
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, IBMC, 15 rue René Descartes, 67000 Strasbourg, France
| | - Maureen R Smith
- Freie Universität Berlin, Department of Mathematics and Computer Science, Arnimallee 6, 14195 Berlin, Germany
| | - Anne-Caroline Jousset
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, IBMC, 15 rue René Descartes, 67000 Strasbourg, France
| | - Laurence Despons
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, IBMC, 15 rue René Descartes, 67000 Strasbourg, France
| | - Géraldine Laumond
- INSERM U1109, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Thomas Decoville
- INSERM U1109, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Pierre Cattenoz
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, IBMC, 15 rue René Descartes, 67000 Strasbourg, France
| | - Christiane Moog
- INSERM U1109, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
| | - Fabrice Jossinet
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, IBMC, 15 rue René Descartes, 67000 Strasbourg, France
| | - Marylène Mougel
- IRIM CNRS UMR9004, Université de Montpellier, Montpellier, France
| | - Jean-Christophe Paillart
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, IBMC, 15 rue René Descartes, 67000 Strasbourg, France
| | - Max von Kleist
- Freie Universität Berlin, Department of Mathematics and Computer Science, Arnimallee 6, 14195 Berlin, Germany
| | - Roland Marquet
- Université de Strasbourg, CNRS, Architecture et Réactivité de l’ARN, UPR 9002, IBMC, 15 rue René Descartes, 67000 Strasbourg, France
| |
Collapse
|
11
|
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.
Collapse
|
12
|
Baeyens A, Naessens E, Van Nuffel A, Weening KE, Reilly AM, Claeys E, Trypsteen W, Vandekerckhove L, Eyckerman S, Gevaert K, Verhasselt B. HIV-1 Vpr N-terminal tagging affects alternative splicing of the viral genome. Sci Rep 2016; 6:34573. [PMID: 27721439 PMCID: PMC5056386 DOI: 10.1038/srep34573] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 09/12/2016] [Indexed: 01/11/2023] Open
Abstract
To facilitate studies on Vpr function in replicating HIV-1, we aimed to tag the protein in an infectious virus. First we showed that N-, but not C-terminal HA/FLAG tagging of Vpr protein preserves Vpr cytopathicity. Cloning the tags into proviral DNA however ablated viral production and replication. By construction of additional viral variants we could show this defect was not protein- but RNA-dependent and sequence specific, and characterized by oversplicing of the genomic RNA. Simulation of genomic RNA folding suggested that introduction of the tag sequence induced an alternative folding structure in a region enriched in splice sites and splicing regulatory sequences. In silico predictions identified the HA/His6-Vpr tagging in HIV-1 to affect mRNA folding less than HA/FLAG-Vpr tagging. In vitro infectivity and mRNA splice pattern improved but did not reach wild-type values. Thus, sequence-specific insertions may interfere with mRNA splicing, possibly due to altered RNA folding. Our results point to the complexity of viral RNA genome sequence interactions. This should be taken into consideration when designing viral manipulation strategies, for both research as for biological interventions.
Collapse
Affiliation(s)
- Ann Baeyens
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University, Ghent, Belgium
| | - Evelien Naessens
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University, Ghent, Belgium
| | - Anouk Van Nuffel
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University, Ghent, Belgium
| | - Karin E Weening
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University, Ghent, Belgium
| | - Anne-Marie Reilly
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University, Ghent, Belgium
| | - Eva Claeys
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University, Ghent, Belgium
| | - Wim Trypsteen
- HIV Translational Research Unit, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Linos Vandekerckhove
- HIV Translational Research Unit, Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Sven Eyckerman
- VIB Medical Biotechnology Center, B-9000 Ghent, Belgium.,Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Kris Gevaert
- VIB Medical Biotechnology Center, B-9000 Ghent, Belgium.,Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium
| | - Bruno Verhasselt
- Department of Clinical Chemistry, Microbiology, and Immunology, Ghent University, Ghent, Belgium
| |
Collapse
|
13
|
A Phylogenetic Survey on the Structure of the HIV-1 Leader RNA Domain That Encodes the Splice Donor Signal. Viruses 2016; 8:v8070200. [PMID: 27455303 PMCID: PMC4974535 DOI: 10.3390/v8070200] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 06/29/2016] [Accepted: 07/01/2016] [Indexed: 11/16/2022] Open
Abstract
RNA splicing is a critical step in the human immunodeficiency virus type 1 (HIV-1) replication cycle because it controls the expression of the complex viral proteome. The major 5′ splice site (5′ss) that is positioned in the untranslated leader of the HIV-1 RNA transcript is of particular interest because it is used for the production of the more than 40 differentially spliced subgenomic mRNAs. HIV-1 splicing needs to be balanced tightly to ensure the proper levels of all viral proteins, including the Gag-Pol proteins that are translated from the unspliced RNA. We previously presented evidence that the major 5′ss is regulated by a repressive local RNA structure, the splice donor (SD) hairpin, that masks the 11 nucleotides (nts) of the 5′ss signal for recognition by U1 small nuclear RNA (snRNA) of the spliceosome machinery. A strikingly different multiple-hairpin RNA conformation was recently proposed for this part of the HIV-1 leader RNA. We therefore inspected the sequence of natural HIV-1 isolates in search for support, in the form of base pair (bp) co-variations, for the different RNA conformations.
Collapse
|
14
|
Mueller N, Klaver B, Berkhout B, Das AT. Human immunodeficiency virus type 1 splicing at the major splice donor site is controlled by highly conserved RNA sequence and structural elements. J Gen Virol 2016; 96:3389-3395. [PMID: 26385834 DOI: 10.1099/jgv.0.000288] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) splicing has to be strictly controlled to ensure the balanced production of the unspliced and all differently spliced viral RNAs. Splicing at the major 59 splice site (59ss) that is used for the synthesis of all spliced RNAs is modulated by the local RNA structure and binding of regulatory SR proteins. Here, we demonstrate that the suboptimal sequence complementarity between this 59ss and U1 small nuclear RNA (snRNA) also contributes to prevent excessive splicing. Analysis of a large set of HIV-1 sequences revealed that all three regulatory features of the 59ss region (RNA structure, SR protein binding and sequence complementarity with U1 snRNA) are highly conserved amongst virus isolates, which supports their importance. Combined mutations that destabilize the local RNA structure, remove binding sites for inhibitory SR proteins and optimize the U1 snRNA complementarity resulted in almost complete splicing and accordingly reduced virus replication.
Collapse
Affiliation(s)
- Nancy Mueller
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Bep Klaver
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Atze T Das
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| |
Collapse
|
15
|
Jain N, Morgan CE, Rife BD, Salemi M, Tolbert BS. Solution Structure of the HIV-1 Intron Splicing Silencer and Its Interactions with the UP1 Domain of Heterogeneous Nuclear Ribonucleoprotein (hnRNP) A1. J Biol Chem 2015; 291:2331-44. [PMID: 26607354 DOI: 10.1074/jbc.m115.674564] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Indexed: 12/11/2022] Open
Abstract
Splicing patterns in human immunodeficiency virus type 1 (HIV-1) are maintained through cis regulatory elements that recruit antagonistic host RNA-binding proteins. The activity of the 3' acceptor site A7 is tightly regulated through a complex network of an intronic splicing silencer (ISS), a bipartite exonic splicing silencer (ESS3a/b), and an exonic splicing enhancer (ESE3). Because HIV-1 splicing depends on protein-RNA interactions, it is important to know the tertiary structures surrounding the splice sites. Herein, we present the NMR solution structure of the phylogenetically conserved ISS stem loop. ISS adopts a stable structure consisting of conserved UG wobble pairs, a folded 2X2 (GU/UA) internal loop, a UU bulge, and a flexible AGUGA apical loop. Calorimetric and biochemical titrations indicate that the UP1 domain of heterogeneous nuclear ribonucleoprotein A1 binds the ISS apical loop site-specifically and with nanomolar affinity. Collectively, this work provides additional insights into how HIV-1 uses a conserved RNA structure to commandeer a host RNA-binding protein.
Collapse
Affiliation(s)
- Niyati Jain
- From the Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106-7078 and
| | - Christopher E Morgan
- From the Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106-7078 and
| | - Brittany D Rife
- Department of Pathology, Immunology, and Laboratory of Medicine, College of Medicine and Emerging Pathogens Institute, University of Florida, Gainesville, Florida 32610-3633
| | - Marco Salemi
- Department of Pathology, Immunology, and Laboratory of Medicine, College of Medicine and Emerging Pathogens Institute, University of Florida, Gainesville, Florida 32610-3633
| | - Blanton S Tolbert
- From the Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106-7078 and
| |
Collapse
|