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Shi X, Zhang Y, Wang Y, Wang J, Gao Y, Wang R, Wang L, Xiong M, Cao Y, Ou N, Liu Q, Ma H, Cai J, Chen H. The tRNA Gm18 methyltransferase TARBP1 promotes hepatocellular carcinoma progression via metabolic reprogramming of glutamine. Cell Death Differ 2024:10.1038/s41418-024-01323-4. [PMID: 38867004 DOI: 10.1038/s41418-024-01323-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 05/29/2024] [Accepted: 05/31/2024] [Indexed: 06/14/2024] Open
Abstract
Cancer cells rely on metabolic reprogramming to sustain the prodigious energetic requirements for rapid growth and proliferation. Glutamine metabolism is frequently dysregulated in cancers and is being exploited as a potential therapeutic target. Using CRISPR/Cas9 interference (CRISPRi) screening, we identified TARBP1 (TAR (HIV-1) RNA Binding Protein 1) as a critical regulator involved in glutamine reliance of cancer cell. Consistent with this discovery, TARBP1 amplification and overexpression are frequently observed in various cancers. Knockout of TARBP1 significantly suppresses cell proliferation, colony formation and xenograft tumor growth. Mechanistically, TARBP1 selectively methylates and stabilizes a small subset of tRNAs, which promotes efficient protein synthesis of glutamine transporter-ASCT2 (also known as SLC1A5) and glutamine import to fuel the growth of cancer cell. Moreover, we found that the gene expression of TARBP1 and ASCT2 are upregulated in combination in clinical cohorts and their upregulation is associated with unfavorable prognosis of HCC (hepatocellular carcinoma). Taken together, this study reveals the unexpected role of TARBP1 in coordinating the tRNA availability and glutamine uptake during HCC progression and provides a potential target for tumor therapy.
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Affiliation(s)
- Xiaoyan Shi
- Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong & Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine; Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yangyi Zhang
- Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong & Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine; Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yuci Wang
- Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong & Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine; Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jie Wang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Institutes of Biomedical Sciences, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, 200032, China
| | - Yang Gao
- Department of Ultrasound, West China Hospital, Sichuan University, Chengdu, 610041, China
- College of Polymer Science and Engineering, Med-X Center for Materials, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, 610065, China
| | - Ruiqi Wang
- Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong & Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine; Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Liyong Wang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Institutes of Biomedical Sciences, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, 200032, China
| | - Minggang Xiong
- Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong & Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine; Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen, 518055, China
- School of Biological Sciences, The University of Hong Kong, Hong Kong, SAR, China
| | - Yanlan Cao
- Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong & Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine; Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Ningjing Ou
- State Key Lab of Reproductive Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Qi Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences; Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Guangzhou, 510640, China.
| | - Honghui Ma
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Institutes of Biomedical Sciences, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, 200032, China.
- Shenzhen Ruipuxun Academy for Stem Cell & Regenerative Medicine, Shenzhen, China.
| | - Jiabin Cai
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Institutes of Biomedical Sciences, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Key Laboratory of Medical Epigenetics and Metabolism, Fudan University, Shanghai, 200032, China.
| | - Hao Chen
- Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong & Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine; Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology, Shenzhen, 518055, China.
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Raines SLM, Falcinelli SD, Peterson JJ, Van Gulck E, Allard B, Kirchherr J, Vega J, Najera I, Boden D, Archin NM, Margolis DM. Nanoparticle delivery of Tat synergizes with classical latency reversal agents to express HIV antigen targets. Antimicrob Agents Chemother 2024:e0020124. [PMID: 38829049 DOI: 10.1128/aac.00201-24] [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: 02/05/2024] [Accepted: 05/10/2024] [Indexed: 06/05/2024] Open
Abstract
Limited cellular levels of the HIV transcriptional activator Tat are one contributor to proviral latency that might be targeted in HIV cure strategies. We recently demonstrated that lipid nanoparticles containing HIV tat mRNA induce HIV expression in primary CD4 T cells. Here, we sought to further characterize tat mRNA in the context of several benchmark latency reversal agents (LRAs), including inhibitor of apoptosis protein antagonists (IAPi), bromodomain and extra-Terminal motif inhibitors (BETi), and histone deacetylase inhibitors (HDACi). tat mRNA reversed latency across several different cell line models of HIV latency, an effect dependent on the TAR hairpin loop. Synergistic enhancement of tat mRNA activity was observed with IAPi, HDACi, and BETi, albeit to variable degrees. In primary CD4 T cells from durably suppressed people with HIV, tat mRNA profoundly increased the frequencies of elongated, multiply-spliced, and polyadenylated HIV transcripts, while having a lesser impact on TAR transcript frequencies. tat mRNAs alone resulted in variable HIV p24 protein induction across donors. However, tat mRNA in combination with IAPi, BETi, or HDACi markedly enhanced HIV RNA and protein expression without overt cytotoxicity or cellular activation. Notably, combination regimens approached or in some cases exceeded the latency reversal activity of maximal mitogenic T cell stimulation. Higher levels of tat mRNA-driven HIV p24 induction were observed in donors with larger mitogen-inducible HIV reservoirs, and expression increased with prolonged exposure time. Combination LRA strategies employing both small molecule inhibitors and Tat delivered to CD4 T cells are a promising approach to effectively target the HIV reservoir.
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Affiliation(s)
- Samuel L M Raines
- Department of Medicine and UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Shane D Falcinelli
- Department of Medicine and UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jackson J Peterson
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Ellen Van Gulck
- Janssen Infectious Diseases, Janssen Research and Development, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Brigitte Allard
- Department of Medicine and UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jennifer Kirchherr
- Department of Medicine and UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jerel Vega
- Arcturus Therapeutics, Science Center Drive, San Diego, California, USA
| | - Isabel Najera
- Janssen Infectious Diseases, Janssen Research and Development, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Daniel Boden
- Janssen Infectious Diseases, Janssen Research and Development, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Nancie M Archin
- Department of Medicine and UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - David M Margolis
- Department of Medicine and UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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Guo X, Liu M, Wang C, Wang Y, Li H, Zhang B, Liu Y, Han J, Wang X, Li T, Li J, Jia L, Li L. The Long Terminal Repeat Sequence of Subtype C and CRF01_AE Recombinants in China. AIDS Res Hum Retroviruses 2023; 39:500-504. [PMID: 37183419 DOI: 10.1089/aid.2022.0175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
HIV-1 provirus is flanked by one long terminal repeat (LTR) at each terminal. The 5' LTR plays important roles in HIV-1 life cycle, especially, it determines HIV-1 transcription. However, there are 810 5' LTR entries exist in the HIV-1 sequence database, accounting for only 0.085% (810/949,484). In this study, we collected plasma samples from HIV-1-infected patients in Shenzhen province and got 219 5' LTR sequences. In addition, we found recombination in the LTR region. The recombinants (LS13145, LS11614, LS14862, and LS14863) possess an insertion of CRF01_AE segment at HXB2 482-630 bp (149 bp) in the skeleton of 5' LTR of subtype C. At the same time, our study found that the occurrence of recombination caused changes in many transcription factor binding sites. As the increasing investigation on 5' LTRs diversity and characterization, we will get a deeper understanding of HIV-1 transmission, evolution, and the basic mechanism of transcriptional regulation.
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Affiliation(s)
- Xing Guo
- Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei, China
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Mengying Liu
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Chunlei Wang
- Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei, China
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Yanglan Wang
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Hanping Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Bohan Zhang
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Yongjian Liu
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Jingwan Han
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Xiaolin Wang
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Tianyi Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Jingyun Li
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Lei Jia
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
| | - Lin Li
- Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei, China
- Department of Virology, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing, China
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Nepal B, Das S, Reith ME, Kortagere S. Overview of the structure and function of the dopamine transporter and its protein interactions. Front Physiol 2023; 14:1150355. [PMID: 36935752 PMCID: PMC10020207 DOI: 10.3389/fphys.2023.1150355] [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: 01/24/2023] [Accepted: 02/21/2023] [Indexed: 03/06/2023] Open
Abstract
The dopamine transporter (DAT) plays an integral role in dopamine neurotransmission through the clearance of dopamine from the extracellular space. Dysregulation of DAT is central to the pathophysiology of numerous neuropsychiatric disorders and as such is an attractive therapeutic target. DAT belongs to the solute carrier family 6 (SLC6) class of Na+/Cl- dependent transporters that move various cargo into neurons against their concentration gradient. This review focuses on DAT (SCL6A3 protein) while extending the narrative to the closely related transporters for serotonin and norepinephrine where needed for comparison or functional relevance. Cloning and site-directed mutagenesis experiments provided early structural knowledge of DAT but our contemporary understanding was achieved through a combination of crystallization of the related bacterial transporter LeuT, homology modeling, and subsequently the crystallization of drosophila DAT. These seminal findings enabled a better understanding of the conformational states involved in the transport of substrate, subsequently aiding state-specific drug design. Post-translational modifications to DAT such as phosphorylation, palmitoylation, ubiquitination also influence the plasma membrane localization and kinetics. Substrates and drugs can interact with multiple sites within DAT including the primary S1 and S2 sites involved in dopamine binding and novel allosteric sites. Major research has centered around the question what determines the substrate and inhibitor selectivity of DAT in comparison to serotonin and norepinephrine transporters. DAT has been implicated in many neurological disorders and may play a role in the pathology of HIV and Parkinson's disease via direct physical interaction with HIV-1 Tat and α-synuclein proteins respectively.
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Affiliation(s)
- Binod Nepal
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Sanjay Das
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Maarten E. Reith
- Department of Psychiatry, New York University School of Medicine, New York City, NY, United States
| | - Sandhya Kortagere
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
- *Correspondence: Sandhya Kortagere,
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Engelman AN, Kvaratskhelia M. Multimodal Functionalities of HIV-1 Integrase. Viruses 2022; 14:926. [PMID: 35632668 PMCID: PMC9144474 DOI: 10.3390/v14050926] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/20/2022] [Accepted: 04/26/2022] [Indexed: 01/11/2023] Open
Abstract
Integrase is the retroviral protein responsible for integrating reverse transcripts into cellular genomes. Co-packaged with viral RNA and reverse transcriptase into capsid-encased viral cores, human immunodeficiency virus 1 (HIV-1) integrase has long been implicated in reverse transcription and virion maturation. However, the underlying mechanisms of integrase in these non-catalytic-related viral replication steps have remained elusive. Recent results have shown that integrase binds genomic RNA in virions, and that mutational or pharmacological disruption of integrase-RNA binding yields eccentric virion particles with ribonucleoprotein complexes situated outside of the capsid shell. Such viruses are defective for reverse transcription due to preferential loss of integrase and viral RNA from infected target cells. Parallel research has revealed defective integrase-RNA binding and eccentric particle formation as common features of class II integrase mutant viruses, a phenotypic grouping of viruses that display defects at steps beyond integration. In light of these new findings, we propose three new subclasses of class II mutant viruses (a, b, and c), all of which are defective for integrase-RNA binding and particle morphogenesis, but differ based on distinct underlying mechanisms exhibited by the associated integrase mutant proteins. We also assess how these findings inform the role of integrase in HIV-1 particle maturation.
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Affiliation(s)
- Alan N. Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA
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Kleinman AJ, Pandrea I, Apetrei C. So Pathogenic or So What?-A Brief Overview of SIV Pathogenesis with an Emphasis on Cure Research. Viruses 2022; 14:135. [PMID: 35062339 PMCID: PMC8781889 DOI: 10.3390/v14010135] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 12/10/2021] [Accepted: 12/25/2021] [Indexed: 02/07/2023] Open
Abstract
HIV infection requires lifelong antiretroviral therapy (ART) to control disease progression. Although ART has greatly extended the life expectancy of persons living with HIV (PWH), PWH nonetheless suffer from an increase in AIDS-related and non-AIDS related comorbidities resulting from HIV pathogenesis. Thus, an HIV cure is imperative to improve the quality of life of PWH. In this review, we discuss the origins of various SIV strains utilized in cure and comorbidity research as well as their respective animal species used. We briefly detail the life cycle of HIV and describe the pathogenesis of HIV/SIV and the integral role of chronic immune activation and inflammation on disease progression and comorbidities, with comparisons between pathogenic infections and nonpathogenic infections that occur in natural hosts of SIVs. We further discuss the various HIV cure strategies being explored with an emphasis on immunological therapies and "shock and kill".
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Affiliation(s)
- Adam J. Kleinman
- Division of Infectious Diseases, DOM, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA;
| | - Ivona Pandrea
- Department of Infectious Diseases and Immunology, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA;
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Cristian Apetrei
- Division of Infectious Diseases, DOM, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA;
- Department of Infectious Diseases and Immunology, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA;
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Wang H, Huang W, Wang Y, Li W, Liu Q, Yin B, Liang L, Wang D, Guan X, Wang L. Enzyme Hinders HIV-1 Tat Viral Transport and Real-Time Measured with Nanopores. ACS Sens 2021; 6:3781-3788. [PMID: 34528798 DOI: 10.1021/acssensors.1c01717] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
HIV-1 Tat protein, an intercellular transporter with a determinant function of delivering "information-rich" molecules in viral multiplication, was tryptic-hydrolyzed and real-time single molecule-monitored in a transmembrane pore. The electrokinetic studies revealed the catalytic and inhibitory effects on enzymatic digestion associated with Ca2+ and Cu2+ ions, respectively, in response to binding interactions with trypsin. Our strategy permits accurate and distinguishable sensing of Ca2+ and Cu2+ via an enzyme assay. In addition, considering the closer mimic of the real situation of HIV spread, measurements in the serum and on cells were also investigated. Transmembrane current measurements together with fluorescence microscopy imaging indicated the potential to perturb the Tat transport in the serum environment and on cells. Because the involved Tat proteolysis should prevent the occurrence of viral delivery, the presented method probably enables efficient hindrance to HIV-1 infection, in complementary to current traditional treatments.
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Affiliation(s)
- Han Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing Key Laboratory of Intelligent Medicine Engineering for Hepatopancreatobiliary Diseases, Chongqing 401147, China
| | - Wenli Huang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Yunjiao Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Wei Li
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Qianshan Liu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Bohua Yin
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
| | - Liyuan Liang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Deqiang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing Key Laboratory of Intelligent Medicine Engineering for Hepatopancreatobiliary Diseases, Chongqing 401147, China
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Pagani I, Poli G, Vicenzi E. TRIM22. A Multitasking Antiviral Factor. Cells 2021; 10:cells10081864. [PMID: 34440633 PMCID: PMC8391480 DOI: 10.3390/cells10081864] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/03/2021] [Accepted: 07/16/2021] [Indexed: 02/06/2023] Open
Abstract
Viral invasion of target cells triggers an immediate intracellular host defense system aimed at preventing further propagation of the virus. Viral genomes or early products of viral replication are sensed by a number of pattern recognition receptors, leading to the synthesis and production of type I interferons (IFNs) that, in turn, activate a cascade of IFN-stimulated genes (ISGs) with antiviral functions. Among these, several members of the tripartite motif (TRIM) family are antiviral executors. This article will focus, in particular, on TRIM22 as an example of a multitarget antiviral member of the TRIM family. The antiviral activities of TRIM22 against different DNA and RNA viruses, particularly human immunodeficiency virus type 1 (HIV-1) and influenza A virus (IAV), will be discussed. TRIM22 restriction of virus replication can involve either direct interaction of TRIM22 E3 ubiquitin ligase activity with viral proteins, or indirect protein–protein interactions resulting in control of viral gene transcription, but also epigenetic effects exerted at the chromatin level.
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Affiliation(s)
- Isabel Pagani
- Viral Pathogenesis and Biosafety Unit, IRCCS-Ospedale San Raffaele, 20132 Milan, Italy;
| | - Guido Poli
- Human Immuno-Virology Unit, IRCCS-Ospedale San Raffaele, 20132 Milan, Italy;
- School of Medicine, Vita-Salute San Raffaele University, 20132 Milan, Italy
| | - Elisa Vicenzi
- Viral Pathogenesis and Biosafety Unit, IRCCS-Ospedale San Raffaele, 20132 Milan, Italy;
- Correspondence:
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Brodyagin N, Katkevics M, Kotikam V, Ryan CA, Rozners E. Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications. Beilstein J Org Chem 2021; 17:1641-1688. [PMID: 34367346 PMCID: PMC8313981 DOI: 10.3762/bjoc.17.116] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/28/2021] [Indexed: 12/23/2022] Open
Abstract
Peptide nucleic acid (PNA) is arguably one of the most successful DNA mimics, despite a most dramatic departure from the native structure of DNA. The present review summarizes 30 years of research on PNA's chemistry, optimization of structure and function, applications as probes and diagnostics, and attempts to develop new PNA therapeutics. The discussion starts with a brief review of PNA's binding modes and structural features, followed by the most impactful chemical modifications, PNA enabled assays and diagnostics, and discussion of the current state of development of PNA therapeutics. While many modifications have improved on PNA's binding affinity and specificity, solubility and other biophysical properties, the original PNA is still most frequently used in diagnostic and other in vitro applications. Development of therapeutics and other in vivo applications of PNA has notably lagged behind and is still limited by insufficient bioavailability and difficulties with tissue specific delivery. Relatively high doses are required to overcome poor cellular uptake and endosomal entrapment, which increases the risk of toxicity. These limitations remain unsolved problems waiting for innovative chemistry and biology to unlock the full potential of PNA in biomedical applications.
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Affiliation(s)
- Nikita Brodyagin
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Martins Katkevics
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
| | - Venubabu Kotikam
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Christopher A Ryan
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
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Ganser LR, Chu CC, Bogerd HP, Kelly ML, Cullen BR, Al-Hashimi HM. Probing RNA Conformational Equilibria within the Functional Cellular Context. Cell Rep 2021; 30:2472-2480.e4. [PMID: 32101729 DOI: 10.1016/j.celrep.2020.02.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 12/24/2019] [Accepted: 01/31/2020] [Indexed: 12/17/2022] Open
Abstract
Low-abundance short-lived non-native conformations referred to as excited states (ESs) are increasingly observed in vitro and implicated in the folding and biological activities of regulatory RNAs. We developed an approach for assessing the relative abundance of RNA ESs within the functional cellular context. Nuclear magnetic resonance (NMR) spectroscopy was used to estimate the degree to which substitution mutations bias conformational equilibria toward the inactive ES in vitro. The cellular activity of the ES-stabilizing mutants was used as an indirect measure of the conformational equilibria within the functional cellular context. Compensatory mutations that restore the ground-state conformation were used to control for changes in sequence. Using this approach, we show that the ESs of two regulatory RNAs from HIV-1, the transactivation response element (TAR) and the Rev response element (RRE), likely form in cells with abundances comparable to those measured in vitro, and their targeted stabilization may provide an avenue for developing anti-HIV therapeutics.
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Affiliation(s)
- Laura R Ganser
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Chia-Chieh Chu
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Hal P Bogerd
- Department of Molecular Genetics and Microbiology, Center for Virology, Duke University Medical Center, Durham, NC 27710, USA
| | - Megan L Kelly
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Bryan R Cullen
- Department of Molecular Genetics and Microbiology, Center for Virology, Duke University Medical Center, Durham, NC 27710, USA.
| | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.
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11
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Yadavar-Nikravesh MS, Milani A, Vahabpour R, Khoobi M, Bakhshandeh H, Bolhassani A. In vitro Anti-HIV-1 Activity of the Recombinant HIV-1 TAT Protein Along With Tenofovir Drug. Curr HIV Res 2021; 19:138-146. [PMID: 33045968 DOI: 10.2174/1570162x18666201012152600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/19/2020] [Accepted: 09/01/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND HIV-1 TAT protein is essential for the regulation of viral genome transcription. The first exon of TAT protein has a fundamental role in the stimulation of the extrinsic and intrinsic apoptosis pathways, but its anti-HIV activity is not clear yet. METHODS In the current study, we firstly cloned the first exon of the TAT coding sequence in the pET-24a expression vector and then protein expression was done in the Rosetta expression host. Next, the expressed TAT protein was purified by Ni-NTA column under native conditions. After that, the protein yield was determined by Bradford kit and NanoDrop spectrophotometry. Finally, the cytotoxicity effect and anti-Scr-HIV-1 activity of the recombinant TAT protein alone and along with Tenofovir drug were assessed by MTT and ELISA, respectively. RESULTS The recombinant TAT protein was successfully generated in E. coli, as confirmed by 13.5% SDS-PAGE and western blotting. The protein yield was ~150-200 μg/ml. In addition, the recombinant TAT protein at a certain dose with low toxicity could suppress Scr-HIV replication in the infected HeLa cells (~30%) that was comparable with a low toxic dose of Tenofovir drug (~40%). It was interesting that the recombinant TAT protein could enhance anti-HIV potency of Tenofovir drug up to 66%. CONCLUSION Generally, a combination of TAT protein and Tenofovir drug could significantly inhibit HIV-1 replication. It will be required to determine their mechanism of action in the next studies.
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Affiliation(s)
| | - Alireza Milani
- Department of Hepatitis, AIDS and Blood Borne Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Rouhollah Vahabpour
- Department of Medical Lab Technology, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences; Tehran, Iran
| | - Mehdi Khoobi
- Department of Pharmaceutical Biomaterials and Medical Biomaterials Research Center (MBRC), Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Haleh Bakhshandeh
- Nanobiotechnology Department, New Technologies Research Group, Pasteur Institute of Iran, Tehran, Iran
| | - Azam Bolhassani
- Department of Hepatitis, AIDS and Blood Borne Diseases, Pasteur Institute of Iran, Tehran, Iran
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12
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The Role of APOBECs in Viral Replication. Microorganisms 2020; 8:microorganisms8121899. [PMID: 33266042 PMCID: PMC7760323 DOI: 10.3390/microorganisms8121899] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 12/14/2022] Open
Abstract
Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) proteins are a diverse and evolutionarily conserved family of cytidine deaminases that provide a variety of functions from tissue-specific gene expression and immunoglobulin diversity to control of viruses and retrotransposons. APOBEC family expansion has been documented among mammalian species, suggesting a powerful selection for their activity. Enzymes with a duplicated zinc-binding domain often have catalytically active and inactive domains, yet both have antiviral function. Although APOBEC antiviral function was discovered through hypermutation of HIV-1 genomes lacking an active Vif protein, much evidence indicates that APOBECs also inhibit virus replication through mechanisms other than mutagenesis. Multiple steps of the viral replication cycle may be affected, although nucleic acid replication is a primary target. Packaging of APOBECs into virions was first noted with HIV-1, yet is not a prerequisite for viral inhibition. APOBEC antagonism may occur in viral producer and recipient cells. Signatures of APOBEC activity include G-to-A and C-to-T mutations in a particular sequence context. The importance of APOBEC activity for viral inhibition is reflected in the identification of numerous viral factors, including HIV-1 Vif, which are dedicated to antagonism of these deaminases. Such viral antagonists often are only partially successful, leading to APOBEC selection for viral variants that enhance replication or avoid immune elimination.
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13
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Yu AM, Choi YH, Tu MJ. RNA Drugs and RNA Targets for Small Molecules: Principles, Progress, and Challenges. Pharmacol Rev 2020; 72:862-898. [PMID: 32929000 PMCID: PMC7495341 DOI: 10.1124/pr.120.019554] [Citation(s) in RCA: 179] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
RNA-based therapies, including RNA molecules as drugs and RNA-targeted small molecules, offer unique opportunities to expand the range of therapeutic targets. Various forms of RNAs may be used to selectively act on proteins, transcripts, and genes that cannot be targeted by conventional small molecules or proteins. Although development of RNA drugs faces unparalleled challenges, many strategies have been developed to improve RNA metabolic stability and intracellular delivery. A number of RNA drugs have been approved for medical use, including aptamers (e.g., pegaptanib) that mechanistically act on protein target and small interfering RNAs (e.g., patisiran and givosiran) and antisense oligonucleotides (e.g., inotersen and golodirsen) that directly interfere with RNA targets. Furthermore, guide RNAs are essential components of novel gene editing modalities, and mRNA therapeutics are under development for protein replacement therapy or vaccination, including those against unprecedented severe acute respiratory syndrome coronavirus pandemic. Moreover, functional RNAs or RNA motifs are highly structured to form binding pockets or clefts that are accessible by small molecules. Many natural, semisynthetic, or synthetic antibiotics (e.g., aminoglycosides, tetracyclines, macrolides, oxazolidinones, and phenicols) can directly bind to ribosomal RNAs to achieve the inhibition of bacterial infections. Therefore, there is growing interest in developing RNA-targeted small-molecule drugs amenable to oral administration, and some (e.g., risdiplam and branaplam) have entered clinical trials. Here, we review the pharmacology of novel RNA drugs and RNA-targeted small-molecule medications, with a focus on recent progresses and strategies. Challenges in the development of novel druggable RNA entities and identification of viable RNA targets and selective small-molecule binders are discussed. SIGNIFICANCE STATEMENT: With the understanding of RNA functions and critical roles in diseases, as well as the development of RNA-related technologies, there is growing interest in developing novel RNA-based therapeutics. This comprehensive review presents pharmacology of both RNA drugs and RNA-targeted small-molecule medications, focusing on novel mechanisms of action, the most recent progress, and existing challenges.
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MESH Headings
- Aptamers, Nucleotide/pharmacology
- Aptamers, Nucleotide/therapeutic use
- Betacoronavirus
- COVID-19
- Chemistry Techniques, Analytical/methods
- Chemistry Techniques, Analytical/standards
- Clustered Regularly Interspaced Short Palindromic Repeats
- Coronavirus Infections/drug therapy
- Drug Delivery Systems/methods
- Drug Development/organization & administration
- Drug Discovery
- Humans
- MicroRNAs/pharmacology
- MicroRNAs/therapeutic use
- Oligonucleotides, Antisense/pharmacology
- Oligonucleotides, Antisense/therapeutic use
- Pandemics
- Pneumonia, Viral/drug therapy
- RNA/adverse effects
- RNA/drug effects
- RNA/pharmacology
- RNA, Antisense/pharmacology
- RNA, Antisense/therapeutic use
- RNA, Messenger/drug effects
- RNA, Messenger/pharmacology
- RNA, Ribosomal/drug effects
- RNA, Ribosomal/pharmacology
- RNA, Small Interfering/pharmacology
- RNA, Small Interfering/therapeutic use
- RNA, Viral/drug effects
- Ribonucleases/metabolism
- Riboswitch/drug effects
- SARS-CoV-2
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Affiliation(s)
- Ai-Ming Yu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, California (A.-M.Y., Y.H.C., M.-J.T.) and College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang-si, Gyonggi-do, Republic of Korea (Y.H.C.)
| | - Young Hee Choi
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, California (A.-M.Y., Y.H.C., M.-J.T.) and College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang-si, Gyonggi-do, Republic of Korea (Y.H.C.)
| | - Mei-Juan Tu
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, Sacramento, California (A.-M.Y., Y.H.C., M.-J.T.) and College of Pharmacy and Integrated Research Institute for Drug Development, Dongguk University-Seoul, Goyang-si, Gyonggi-do, Republic of Korea (Y.H.C.)
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14
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Ventura JD. Human Immunodeficiency Virus 1 (HIV-1): Viral Latency, the Reservoir, and the Cure. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2020; 93:549-560. [PMID: 33005119 PMCID: PMC7513431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
An estimated 37 million people globally suffer from Human Immunodeficiency Virus-1 (HIV-1) infection with 1.7 million newly acquired infections occurring on average each year. Although crucial advances in combined antiretroviral therapy (ART) over the last two decades have transformed an HIV-1 diagnosis into a tolerable and controlled condition, enabling over 20 million people living with HIV-1 to enjoy healthy and productive lives, no cure or vaccine yet exists. Developing a successful cure strategy will require a firm understanding of how viral latency is established and how a persistent and long-lived latent is generated. The latent reservoir remains the primary obstacle for cure development and most putative cure strategies proposed fundamentally address its eradication or permanent suppression.
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Affiliation(s)
- John D. Ventura
- To whom all correspondence should be addressed:
Dr. John D. Ventura, . ORCID iD:
https://orcid.org/0000-0002-4373-3242.
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15
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Dick A, Cocklin S. Bioisosteric Replacement as a Tool in Anti-HIV Drug Design. Pharmaceuticals (Basel) 2020; 13:ph13030036. [PMID: 32121077 PMCID: PMC7151723 DOI: 10.3390/ph13030036] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 12/22/2022] Open
Abstract
Bioisosteric replacement is a powerful tool for modulating the drug-like properties, toxicity, and chemical space of experimental therapeutics. In this review, we focus on selected cases where bioisosteric replacement and scaffold hopping have been used in the development of new anti-HIV-1 therapeutics. Moreover, we cover field-based, computational methodologies for bioisosteric replacement, using studies from our group as an example. It is our hope that this review will serve to highlight the utility and potential of bioisosteric replacement in the continuing search for new and improved anti-HIV drugs.
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Affiliation(s)
| | - Simon Cocklin
- Correspondence: ; Tel.: +215-762-7234 or +215-762-4979
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16
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Abstract
RNA recognition frequently results in conformational changes that optimize intermolecular binding. As a consequence, the overall binding affinity of RNA to its binding partners depends not only on the intermolecular interactions formed in the bound state but also on the energy cost associated with changing the RNA conformational distribution. Measuring these "conformational penalties" is, however, challenging because bound RNA conformations tend to have equilibrium populations in the absence of the binding partner that fall outside detection by conventional biophysical methods. In this study we employ as a model system HIV-1 TAR RNA and its interaction with the ligand argininamide (ARG), a mimic of TAR's cognate protein binding partner, the transactivator Tat. We use NMR chemical shift perturbations and relaxation dispersion in combination with Bayesian inference to develop a detailed thermodynamic model of coupled conformational change and ligand binding. Starting from a comprehensive 12-state model of the equilibrium, we estimate the energies of six distinct detectable thermodynamic states that are not accessible by currently available methods. Our approach identifies a minimum of four RNA intermediates that differ in terms of the TAR conformation and ARG occupancy. The dominant bound TAR conformation features two bound ARG ligands and has an equilibrium population in the absence of ARG that is below detection limit. Consequently, even though ARG binds to TAR with an apparent overall weak affinity (Kdapp ≈ 0.2 mM), it binds the prefolded conformation with a Kd in the nM range. Our results show that conformational penalties can be major determinants of RNA-ligand binding affinity as well as a source of binding cooperativity, with important implications for a predictive understanding of how RNA is recognized and for RNA-targeted drug discovery.
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Affiliation(s)
- Nicole I. Orlovsky
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - Hashim M. Al-Hashimi
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Terrence G. Oas
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, United States
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
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17
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Tsai CH, Whiteley CG, Lee DJ. Interactions between HIV-1 protease, silver nanoparticles, and specific peptides. J Taiwan Inst Chem Eng 2019. [DOI: 10.1016/j.jtice.2019.07.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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18
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Withers JB, Mondol V, Pawlica P, Rosa-Mercado NA, Tycowski KT, Ghasempur S, Torabi SF, Steitz JA. Idiosyncrasies of Viral Noncoding RNAs Provide Insights into Host Cell Biology. Annu Rev Virol 2019; 6:297-317. [PMID: 31039329 PMCID: PMC6768742 DOI: 10.1146/annurev-virology-092818-015811] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Like their host cells, many viruses express noncoding RNAs (ncRNAs). Despite the technical challenge of ascribing function to ncRNAs, diverse biological roles for virally expressed ncRNAs have been described, including regulation of viral replication, modulation of host gene expression, host immune evasion, cellular survival, and cellular transformation. Insights into conserved interactions between viral ncRNAs and host cell machinery frequently lead to novel findings concerning host cell biology. In this review, we discuss the functions and biogenesis of ncRNAs produced by animal viruses. Specifically, we describe noncanonical pathways of microRNA (miRNA) biogenesis and novel mechanisms used by viruses to manipulate miRNA and messenger RNA stability. We also highlight recent advances in understanding the function of viral long ncRNAs and circular RNAs.
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Affiliation(s)
- Johanna B Withers
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
- Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA
| | - Vanessa Mondol
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
| | - Paulina Pawlica
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
| | - Nicolle A Rosa-Mercado
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
| | - Kazimierz T Tycowski
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
- Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA
| | - Salehe Ghasempur
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
| | - Seyed F Torabi
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA; , , , , , , ,
- Howard Hughes Medical Institute, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, Connecticut 06536, USA
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19
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Rojas VK, Park IW. Role of the Ubiquitin Proteasome System (UPS) in the HIV-1 Life Cycle. Int J Mol Sci 2019; 20:ijms20122984. [PMID: 31248071 PMCID: PMC6628307 DOI: 10.3390/ijms20122984] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/10/2019] [Accepted: 06/11/2019] [Indexed: 01/18/2023] Open
Abstract
Given that the ubiquitin proteasome system (UPS) is the major protein degradation process in the regulation of a wide variety of cellular processes in eukaryotic cells, including alteration of cellular location, modulation of protein activity, and regulation of protein interaction, it is reasonable to suggest that the infecting HIV-1 and the invaded hosts exploit the UPS in a contest for survival and proliferation. However, to date, regulation of the HIV-1 life cycle has been mainly explained by the stage-specific expression of HIV-1 viral genes, not by elimination processes of the synthesized proteins after completion of their duties in the infected cells, which is also quintessential for understanding the molecular processes of the virus life cycle and thereby HIV-1 pathogenesis. In fact, several previous publications have indicated that the UPS plays a critical role in the regulation of the proteasomal degradation of viral and cellular counterparts at every step of the HIV-1 life cycle, from the virus entry to release of the assembled virus particles, which is integral for the regulation of survival and proliferation of the infecting HIV-1 and to replication restriction of the invading virus in the host. However, it is unknown whether and how these individual events taking place at different stages of the HIV-1 life cycle are orchestrated as an overall strategy to overcome the restrictions conferred by the host cells. Thus, in this review, we overview the interplay between HIV-1 viral and cellular proteins for restrictions/competitions for proliferation of the virus in the infected cell, which could open a new avenue for the development of therapeutics against HIV-1 via targeting a specific step of the proteasome degradation pathway during the HIV-1 life cycle.
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Affiliation(s)
- Vivian K Rojas
- Department of Microbiology, Immunology, and Genetics, University of North Texas, Health Science Center, Fort Worth, TX 76107, USA.
| | - In-Woo Park
- Department of Microbiology, Immunology, and Genetics, University of North Texas, Health Science Center, Fort Worth, TX 76107, USA.
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20
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Chavali SS, Bonn-Breach R, Wedekind JE. Face-time with TAR: Portraits of an HIV-1 RNA with diverse modes of effector recognition relevant for drug discovery. J Biol Chem 2019; 294:9326-9341. [PMID: 31080171 DOI: 10.1074/jbc.rev119.006860] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Small molecules and short peptides that potently and selectively bind RNA are rare, making the molecular structures of these complexes highly exceptional. Accordingly, several recent investigations have provided unprecedented structural insights into how peptides and proteins recognize the HIV-1 transactivation response (TAR) element, a 59-nucleotide-long, noncoding RNA segment in the 5' long terminal repeat region of viral transcripts. Here, we offer an integrated perspective on these advances by describing earlier progress on TAR binding to small molecules, and by drawing parallels to recent successes in the identification of compounds that target the hepatitis C virus internal ribosome entry site (IRES) and the flavin-mononucleotide riboswitch. We relate this work to recent progress that pinpoints specific determinants of TAR recognition by: (i) viral Tat proteins, (ii) an innovative lab-evolved TAR-binding protein, and (iii) an ultrahigh-affinity cyclic peptide. New structural details are used to model the TAR-Tat-super-elongation complex (SEC) that is essential for efficient viral transcription and represents a focal point for antiviral drug design. A key prediction is that the Tat transactivation domain makes modest contacts with the TAR apical loop, whereas its arginine-rich motif spans the entire length of the TAR major groove. This expansive interface has significant implications for drug discovery and design, and it further suggests that future lab-evolved proteins could be deployed to discover steric restriction points that block Tat-mediated recruitment of the host SEC to HIV-1 TAR.
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Affiliation(s)
- Sai Shashank Chavali
- From the Department of Biochemistry and Biophysics, Center for RNA Biology, and Center for AIDS Research, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
| | - Rachel Bonn-Breach
- From the Department of Biochemistry and Biophysics, Center for RNA Biology, and Center for AIDS Research, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
| | - Joseph E Wedekind
- From the Department of Biochemistry and Biophysics, Center for RNA Biology, and Center for AIDS Research, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642
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21
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Falkenhagen A, Joshi S. Genetic Strategies for HIV Treatment and Prevention. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 13:514-533. [PMID: 30388625 PMCID: PMC6205348 DOI: 10.1016/j.omtn.2018.09.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 08/28/2018] [Accepted: 09/02/2018] [Indexed: 01/02/2023]
Abstract
Conventional HIV gene therapy approaches are based on engineering HIV target cells that are non-permissive to viral replication. However, expansion of gene-modified HIV target cells has been limited in patients. Alternative genetic strategies focus on generating gene-modified producer cells that secrete antiviral proteins (AVPs). The secreted AVPs interfere with HIV entry, and, therefore, they extend the protection against infection to unmodified HIV target cells. Since any cell type can potentially secrete AVPs, hematopoietic and non-hematopoietic cell lineages can function as producer cells. Secretion of AVPs from non-hematopoietic cells opens the possibility of using a genetic approach for HIV prevention. Another strategy aims at modifying cytotoxic T cells to selectively target and eliminate infected cells. This review provides an overview of the different genetic approaches for HIV treatment and prevention.
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Affiliation(s)
- Alexander Falkenhagen
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Sadhna Joshi
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada.
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22
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Structural mechanism for HIV-1 TAR loop recognition by Tat and the super elongation complex. Proc Natl Acad Sci U S A 2018; 115:12973-12978. [PMID: 30514815 DOI: 10.1073/pnas.1806438115] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Promoter-proximal pausing by RNA polymerase II (Pol II) is a key regulatory step in human immunodeficiency virus-1 (HIV-1) transcription and thus in the reversal of HIV latency. By binding to the nascent transactivating response region (TAR) RNA, HIV-1 Tat recruits the human super elongation complex (SEC) to the promoter and releases paused Pol II. Structural studies of TAR interactions have been largely focused on interactions between the TAR bulge and the arginine-rich motif (ARM) of Tat. Here, the crystal structure of the TAR loop in complex with Tat and the SEC core was determined at a 3.5-Å resolution. The bound TAR loop is stabilized by cross-loop hydrogen bonds. It makes structure-specific contacts with the side chains of the Cyclin T1 Tat-TAR recognition motif (TRM) and the zinc-coordinating loop of Tat. The TAR loop phosphate backbone forms electrostatic and VDW interactions with positively charged side chains of the CycT1 TRM. Mutational analysis showed that these interactions contribute importantly to binding affinity. The Tat ARM was present in the crystallized construct; however, it was not visualized in the electron density, and the TAR bulge was not formed in the RNA construct used in crystallization. Binding assays showed that TAR bulge-Tat ARM interactions contribute less to TAR binding affinity than TAR loop interactions with the CycT1 TRM and Tat core. Thus, the TAR loop evolved to make high-affinity interactions with the TRM while Tat has three roles: scaffolding and stabilizing the TRM, making specific interactions through its zinc-coordinating loop, and making electrostatic interactions through its ARM.
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23
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Belashov IA, Crawford DW, Cavender CE, Dai P, Beardslee PC, Mathews DH, Pentelute BL, McNaughton BR, Wedekind JE. Structure of HIV TAR in complex with a Lab-Evolved RRM provides insight into duplex RNA recognition and synthesis of a constrained peptide that impairs transcription. Nucleic Acids Res 2018; 46:6401-6415. [PMID: 29961805 PMCID: PMC6061845 DOI: 10.1093/nar/gky529] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 05/23/2018] [Accepted: 05/25/2018] [Indexed: 12/22/2022] Open
Abstract
Natural and lab-evolved proteins often recognize their RNA partners with exquisite affinity. Structural analysis of such complexes can offer valuable insight into sequence-selective recognition that can be exploited to alter biological function. Here, we describe the structure of a lab-evolved RNA recognition motif (RRM) bound to the HIV-1 trans-activation response (TAR) RNA element at 1.80 Å-resolution. The complex reveals a trio of arginines in an evolved β2-β3 loop penetrating deeply into the major groove to read conserved guanines while simultaneously forming cation-π and salt-bridge contacts. The observation that the evolved RRM engages TAR within a double-stranded stem is atypical compared to most RRMs. Mutagenesis, thermodynamic analysis and molecular dynamics validate the atypical binding mode and quantify molecular contributions that support the exceptionally tight binding of the TAR-protein complex (KD,App of 2.5 ± 0.1 nM). These findings led to the hypothesis that the β2-β3 loop can function as a standalone TAR-recognition module. Indeed, short constrained peptides comprising the β2-β3 loop still bind TAR (KD,App of 1.8 ± 0.5 μM) and significantly weaken TAR-dependent transcription. Our results provide a detailed understanding of TAR molecular recognition and reveal that a lab-evolved protein can be reduced to a minimal RNA-binding peptide.
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Affiliation(s)
- Ivan A Belashov
- Department of Biochemistry & Biophysics, Center for RNA Biology, and Center for AIDS Research, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
| | - David W Crawford
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
| | - Chapin E Cavender
- Department of Biochemistry & Biophysics, Center for RNA Biology, and Center for AIDS Research, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
| | - Peng Dai
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Patrick C Beardslee
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
| | - David H Mathews
- Department of Biochemistry & Biophysics, Center for RNA Biology, and Center for AIDS Research, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02139, USA
| | - Brian R McNaughton
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Joseph E Wedekind
- Department of Biochemistry & Biophysics, Center for RNA Biology, and Center for AIDS Research, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA
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Rice AP. The HIV-1 Tat Protein: Mechanism of Action and Target for HIV-1 Cure Strategies. Curr Pharm Des 2018; 23:4098-4102. [PMID: 28677507 DOI: 10.2174/1381612823666170704130635] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 06/12/2017] [Accepted: 06/20/2017] [Indexed: 02/07/2023]
Abstract
The general mechanism involved in Tat activation of RNA Polymerase II (RNAP II) elongation of the integrated HIV-1 was elucidated over 20 years ago. This mechanism involves Tat binding to the TAR RNA element that forms at the 5' end of viral transcripts and recruiting a general RNAP II elongation factor termed as PTEFb. This elongation factor consists of CDK9 and Cyclin T1, and when recruited by Tat to TAR RNA, CDK9 was proposed to phosphorylate the carboxyl terminal domain of RNAP II and thereby activate elongation. Research in the past two decades has shown that the mechanism of Tat action is considerably more complicated than this simple model. In metabolically active cells, CDK9 and Cyclin T1 are now known to be largely sequestered in a RNA-protein complex termed the 7SK RNP. CDK9 and Cyclin T1 are released from the 7SK RNP by mechanisms not yet fully elucidated and along with Tat, bind to TAR RNA and orchestrate the assembly of a Super Elongation Complex (SEC) containing several additional proteins. CDK9 in the SEC then phosphorylates multiple substrates in the RNAP II complex to activate elongation. Importantly for therapeutic strategies, CDK9 and Cyclin T1 functions are down-regulated in resting CD4+ T cells that harbor latent HIV-1, and their up-regulation is required for reactivation of latent virus. Current strategies for a functional cure of HIV-1 infection therefore are likely to require development of latency reversal agents that up-regulate CDK9 and Cyclin T1 function in resting CD4+ T cells.
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Affiliation(s)
- Andrew P Rice
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030. United States
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25
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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.
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26
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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.
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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
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Sengupta S, Siliciano RF. Targeting the Latent Reservoir for HIV-1. Immunity 2018; 48:872-895. [PMID: 29768175 PMCID: PMC6196732 DOI: 10.1016/j.immuni.2018.04.030] [Citation(s) in RCA: 233] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 04/26/2018] [Accepted: 04/26/2018] [Indexed: 02/07/2023]
Abstract
Antiretroviral therapy can effectively block HIV-1 replication and prevent or reverse immunodeficiency in HIV-1-infected individuals. However, viral replication resumes within weeks of treatment interruption. The major barrier to a cure is a small pool of resting memory CD4+ T cells that harbor latent HIV-1 proviruses. This latent reservoir is now the focus of an intense international research effort. We describe how the reservoir is established, challenges involved in eliminating it, and pharmacologic and immunologic strategies for targeting this reservoir. The development of a successful cure strategy will most likely require understanding the mechanisms that maintain HIV-1 proviruses in a latent state and pathways that drive the proliferation of infected cells, which slows reservoir decay. In addition, a cure will require the development of effective immunologic approaches to eliminating infected cells. There is renewed optimism about the prospect of a cure, and the interventions discussed here could pave the way.
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Affiliation(s)
- Srona Sengupta
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Graduate Program in Immunology and Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Robert F Siliciano
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Baltimore, MD 21205, USA.
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28
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Maderna E, Colombo L, Cagnotto A, Di Fede G, Indaco A, Tagliavini F, Salmona M, Giaccone G. In Situ Tissue Labeling of Cerebral Amyloid Using HIV-Related Tat Peptide. Mol Neurobiol 2018; 55:6834-6840. [PMID: 29349578 DOI: 10.1007/s12035-018-0870-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 01/07/2018] [Indexed: 11/25/2022]
Abstract
Delivering peptide-based drugs to the brain is a major challenge because of the existence of the blood-brain barrier (BBB). To overcome this problem, cell-penetrating peptides derived from proteins that are able to cross biological membranes have been used as cell-permeable and brain-penetrant compounds. An example is the transactivator of transcription protein transduction domain (Tat) of the human immunodeficiency virus. The basic domain of Tat is formed of arginine and lysine amino acid residues. Tat has been used as brain-penetrant carrier also in therapies for Alzheimer disease (AD), the most common form of dementia characterized by extracellular cerebral deposits of amyloid made up of Aβ peptide. The aim of our study was to assess whether Tat bind to amyloid deposits of AD and other amyloidoses. An in situ labeling using biotinylated Tat 48-57 peptide was employed in the brain tissue with amyloid deposits made up of Aβ (patients with AD and transgenic AD mice), of prion protein (patients with Gerstmann-Straussler-Scheinker disease), and other amyloidosis, processed by different fixations and pretreatments of histological sections. Our results showed that Tat peptide binds amyloid deposits made up of Aβ, PrP, and immunoglobulin lambda chains in the brain and other tissues processed by alcoholic fixatives but not in formalin-fixed tissue. The fact that biotinylated Tat peptide stains amyloid of different biochemical composition and the specific charge characteristics of the molecules suggests that Tat may bind to heparan sulfate glicosaminoglicans, that are present in amyloid deposits. Inhibition of the binding by Tat pre-incubation with protamine reinforces this hypothesis. Binding of Tat to amyloid deposits should be kept in mind in interpreting the results of studies employing this molecule as brain-penetrating compound for the treatment of cerebral amyloidoses. Our results also suggest that Tat may be helpful for the analysis of the mechanisms of amyloidogenesis, and in particular, the interactions between specific amyloid peptides and glicosaminoglicans.
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Affiliation(s)
- E Maderna
- Neuropathology - Neurology V Unit, IRCCS Foundation "Carlo Besta" Neurological Institute, Via Celoria 11, 20133, Milan, Italy.
| | - L Colombo
- Department of Molecular Biochemistry and Pharmacology, IRCCS Istituto di Ricerche Farmacologiche "Mario Negri", Via La Masa 19, 20156, Milan, Italy
| | - A Cagnotto
- Department of Molecular Biochemistry and Pharmacology, IRCCS Istituto di Ricerche Farmacologiche "Mario Negri", Via La Masa 19, 20156, Milan, Italy
| | - G Di Fede
- Neuropathology - Neurology V Unit, IRCCS Foundation "Carlo Besta" Neurological Institute, Via Celoria 11, 20133, Milan, Italy
| | - A Indaco
- Neuropathology - Neurology V Unit, IRCCS Foundation "Carlo Besta" Neurological Institute, Via Celoria 11, 20133, Milan, Italy
| | - F Tagliavini
- Neuropathology - Neurology V Unit, IRCCS Foundation "Carlo Besta" Neurological Institute, Via Celoria 11, 20133, Milan, Italy
| | - M Salmona
- Department of Molecular Biochemistry and Pharmacology, IRCCS Istituto di Ricerche Farmacologiche "Mario Negri", Via La Masa 19, 20156, Milan, Italy
| | - G Giaccone
- Neuropathology - Neurology V Unit, IRCCS Foundation "Carlo Besta" Neurological Institute, Via Celoria 11, 20133, Milan, Italy
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Noncoding RNAs in Retrovirus Replication. RETROVIRUS-CELL INTERACTIONS 2018. [PMCID: PMC7173536 DOI: 10.1016/b978-0-12-811185-7.00012-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Although a limited percentage of the genome produces proteins, approximately 90% is transcribed, indicating important roles for noncoding RNA (ncRNA). It is now known that these ncRNAs have a multitude of cellular functions ranging from the regulation of gene expression to roles as structural elements in ribonucleoprotein complexes. ncRNA is also represented at nearly every step of viral life cycles. This chapter will focus on ncRNAs of both host and viral origin and their roles in retroviral life cycles. Cellular ncRNA represents a significant portion of material packaged into retroviral virions and includes transfer RNAs, 7SL RNA, U RNA, and vault RNA. Initially thought to be random packaging events, these host RNAs are now proposed to contribute to viral assembly and infectivity. Within the cell, long ncRNA and endogenous retroviruses have been found to regulate aspects of the retroviral life cycle in diverse ways. Additionally, the HIV-1 transactivating response element RNA is thought to impact viral infection beyond the well-characterized role as a transcription activator. RNA interference, thought to be an early version of the innate immune response to viral infection, can still be observed in plants and invertebrates today. The ability of retroviral infection to manipulate the host RNAi pathway is described here. Finally, RNA-based therapies, including gene editing approaches, are being explored as antiretroviral treatments and are discussed.
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30
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Ronsard L, Rai T, Rai D, Ramachandran VG, Banerjea AC. In silico Analyses of Subtype Specific HIV-1 Tat-TAR RNA Interaction Reveals the Structural Determinants for Viral Activity. Front Microbiol 2017; 8:1467. [PMID: 28848502 PMCID: PMC5550727 DOI: 10.3389/fmicb.2017.01467] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 07/20/2017] [Indexed: 11/24/2022] Open
Abstract
HIV-1 Tat transactivates viral genes through strong interaction with TAR RNA. The stem-loop bulged region of TAR consisting of three nucleotides at the position 23–25 and the loop region consisting of six nucleotides at the position 30–35 are essential for viral transactivation. The arginine motif of Tat (five arginine residues on subtype TatC) is critically important for TAR interaction. Any mutations in this motif could lead to reduce transactivation ability and pathogenesis. Here, we identified structurally important residues (arginine and lysine residues) of Tat in this motif could bind to TAR via hydrogen bond interactions which is critical for transactivation. Natural mutant Ser46Phe in the core motif could likely led to conformational change resulting in more hydrogen bond interactions than the wild type Tat making it highly potent transactivator. Importantly, we report the possible probabilities of number of hydrogen bond interactions in the wild type Tat and the mutants with TAR complexes. This study revealed the differential transactivation of subtype B and C Tat could likely be due to the varying number of hydrogen bonds with TAR. Our data support that the N-terminal and the C-terminal domains of Tat is involved in the TAR interactions through hydrogen bonds which is important for transactivation. This study highlights the evolving pattern of structurally important determinants of Tat in the arginine motif for viral transactivation.
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Affiliation(s)
- Larance Ronsard
- Laboratory of Virology, National Institute of ImmunologyNew Delhi, India.,Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur HospitalNew Delhi, India
| | - Tripti Rai
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical SciencesNew Delhi, India
| | - Devesh Rai
- Department of Microbiology, All India Institute of Medical SciencesNew Delhi, India
| | - Vishnampettai G Ramachandran
- Department of Microbiology, University College of Medical Sciences and Guru Teg Bahadur HospitalNew Delhi, India
| | - Akhil C Banerjea
- Laboratory of Virology, National Institute of ImmunologyNew Delhi, India
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31
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The Fragment HMGA2-sh-3p20 from HMGA2 mRNA 3'UTR Promotes the Growth of Hepatoma Cells by Upregulating HMGA2. Sci Rep 2017; 7:2070. [PMID: 28522832 PMCID: PMC5437003 DOI: 10.1038/s41598-017-02311-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 04/10/2017] [Indexed: 01/12/2023] Open
Abstract
High mobility group A2 (HMGA2) plays a crucial role in the development of cancer. However, the mechanism by which HMGA2 promotes the growth of hepatocellular carcinoma (HCC) remains unclear. Here, we explore the hypothesis that HMGA2 may enhance the growth of hepatoma cells through a fragment based on the secondary structure of HMGA2 mRNA 3′-untranslated region (3′UTR). Bioinformatics analysis showed that HMGA2 mRNA displayed a hairpin structure within its 3′UTR, termed HMGA2-sh. Mechanistically, RNA immunoprecipitation assays showed that the microprocessor Drosha or DGCR8 interacted with HMGA2 mRNA in hepatoma cells. Then, Dicer contributes to the generation of the fragment HMGA2-sh-3p20 from the HMGA2-sh. HMGA2-sh-3p20 was screened by PCR analysis. Interestingly, HMGA2-sh-3p20 increased the expression of HMGA2 through antagonizing the tristetraprolin (TTP)-mediated degradation of HMGA2. HMGA2-sh-3p20 inhibited the expression of PTEN by targeting the 3′UTR of PTEN mRNA. In addition, the overexpression of PTEN could downregulate HMGA2 expression. Significantly, we documented the ability of HMGA2-sh-3p20 to promote the growth of hepatoma cells in vitro and in vivo. Thus, we conclude that the fragment HMGA2-sh-3p20 from HMGA2 mRNA 3′UTR promotes the growth of hepatoma cells by upregulating HMGA2. Our finding provides new insights into the mechanism by which HMGA2 enhances hepatocarcinogenesis.
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32
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Kamori D, Ueno T. HIV-1 Tat and Viral Latency: What We Can Learn from Naturally Occurring Sequence Variations. Front Microbiol 2017; 8:80. [PMID: 28194140 PMCID: PMC5276809 DOI: 10.3389/fmicb.2017.00080] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 01/11/2017] [Indexed: 01/25/2023] Open
Abstract
Despite the effective use of antiretroviral therapy, the remainder of a latently HIV-1-infected reservoir mainly in the resting memory CD4+ T lymphocyte subset has provided a great setback toward viral eradication. While host transcriptional silencing machinery is thought to play a dominant role in HIV-1 latency, HIV-1 protein such as Tat, may affect both the establishment and the reversal of latency. Indeed, mutational studies have demonstrated that insufficient Tat transactivation activity can result in impaired transcription of viral genes and the establishment of latency in cell culture experiments. Because Tat protein is one of highly variable proteins within HIV-1 proteome, it is conceivable that naturally occurring Tat mutations may differentially modulate Tat functions, thereby influencing the establishment and/or the reversal of viral latency in vivo. In this mini review, we summarize the recent findings of Tat naturally occurring polymorphisms associating with host immune responses and we highlight the implication of Tat sequence variations in relation to HIV latency.
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Affiliation(s)
- Doreen Kamori
- Center for AIDS Research, Kumamoto University Kumamoto, Japan
| | - Takamasa Ueno
- Center for AIDS Research, Kumamoto UniversityKumamoto, Japan; International Research Center for Medical Sciences, Kumamoto UniversityKumamoto, Japan
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33
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Palangat M, Larson DR. Single-gene dual-color reporter cell line to analyze RNA synthesis in vivo. Methods 2016; 103:77-85. [PMID: 27068658 PMCID: PMC7781226 DOI: 10.1016/j.ymeth.2016.04.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 04/07/2016] [Indexed: 10/22/2022] Open
Abstract
RNA synthesis occurs through the multi-step process of transcription which consists of initiation, elongation, termination, and cleavage of the nascent RNA. In recent years, post-initiation events have attracted considerable attention as regulatory steps in gene expression. In particular, changes in elongation rate have been proposed to alter RNA fate either through changes in RNA secondary structure or recruitment of trans-acting factors, but systematic approaches for perturbing and measuring elongation rate are currently lacking. Here, we describe a system for precisely measuring elongation dynamics for single nascent transcripts at a single gene locus in human cell lines. The system is based on observing the production of fluorescently labeled RNA stem loops which flank a region of interest. The region of interest can be altered using flp recombinases, thus allowing one to study the effects of cis-acting sequences on transcription rate. The dual-color RNAs which are made during this process are exported and translated, thus enabling visualization of each step in gene expression.
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Affiliation(s)
- Murali Palangat
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Daniel R Larson
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States.
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34
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Kingsman SM, Kingsman AJ. Targets for Antiviral Chemotherapy: HIV Regulatory Proteins. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029000100202] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- S. M. Kingsman
- Department of Biochemistry, South Parks Road, Coxford OX1 3QU
| | - A. J. Kingsman
- Department of Biochemistry, South Parks Road, Coxford OX1 3QU
- British Biotechnology Ltd, Watlington Road, Cowley, Oxford, UK
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35
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Hayash T. Preventive effect of ascorbic acid against biological function of human immunodeficiency virus trans-activator of transcription. JOURNAL OF COMPLEMENTARY MEDICINE RESEARCH 2016; 5:205-9. [PMID: 27104044 PMCID: PMC4835998 DOI: 10.5455/jice.20160316010322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/16/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Takuma Hayash
- Department of Immunology and Infectious Disease, Shinshu University School of Medicine, Japan
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36
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Chen Y, Maskri O, Chaminade F, René B, Benkaroun J, Godet J, Mély Y, Mauffret O, Fossé P. Structural Insights into the HIV-1 Minus-strand Strong-stop DNA. J Biol Chem 2016; 291:3468-82. [PMID: 26668324 DOI: 10.1074/jbc.m115.708099] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Indexed: 11/06/2022] Open
Abstract
An essential step of human immunodeficiency virus type 1 (HIV-1) reverse transcription is the first strand transfer that requires base pairing of the R region at the 3'-end of the genomic RNA with the complementary r region at the 3'-end of minus-strand strong-stop DNA (ssDNA). HIV-1 nucleocapsid protein (NC) facilitates this annealing process. Determination of the ssDNA structure is needed to understand the molecular basis of NC-mediated genomic RNA-ssDNA annealing. For this purpose, we investigated ssDNA using structural probes (nucleases and potassium permanganate). This study is the first to determine the secondary structure of the full-length HIV-1 ssDNA in the absence or presence of NC. The probing data and phylogenetic analysis support the folding of ssDNA into three stem-loop structures and the presence of four high-affinity binding sites for NC. Our results support a model for the NC-mediated annealing process in which the preferential binding of NC to four sites triggers unfolding of the three-dimensional structure of ssDNA, thus facilitating interaction of the r sequence of ssDNA with the R sequence of the genomic RNA. In addition, using gel retardation assays and ssDNA mutants, we show that the NC-mediated annealing process does not rely on a single pathway (zipper intermediate or kissing complex).
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Affiliation(s)
- Yingying Chen
- From the LBPA, ENS Cachan, CNRS, Université Paris-Saclay, 61 avenue du Président Wilson, 94235 Cachan cedex, France, the School of Life Sciences, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China, and
| | - Ouerdia Maskri
- From the LBPA, ENS Cachan, CNRS, Université Paris-Saclay, 61 avenue du Président Wilson, 94235 Cachan cedex, France
| | - Françoise Chaminade
- From the LBPA, ENS Cachan, CNRS, Université Paris-Saclay, 61 avenue du Président Wilson, 94235 Cachan cedex, France
| | - Brigitte René
- From the LBPA, ENS Cachan, CNRS, Université Paris-Saclay, 61 avenue du Président Wilson, 94235 Cachan cedex, France
| | - Jessica Benkaroun
- From the LBPA, ENS Cachan, CNRS, Université Paris-Saclay, 61 avenue du Président Wilson, 94235 Cachan cedex, France
| | - Julien Godet
- the Laboratoire de Biophotonique et Pharmacologie, UMR-CNRS 7213, Faculté de Pharmacie, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch-Cedex, France
| | - Yves Mély
- the Laboratoire de Biophotonique et Pharmacologie, UMR-CNRS 7213, Faculté de Pharmacie, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch-Cedex, France
| | - Olivier Mauffret
- From the LBPA, ENS Cachan, CNRS, Université Paris-Saclay, 61 avenue du Président Wilson, 94235 Cachan cedex, France
| | - Philippe Fossé
- From the LBPA, ENS Cachan, CNRS, Université Paris-Saclay, 61 avenue du Président Wilson, 94235 Cachan cedex, France,
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37
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Yang T, Li S, Zhang X, Pang X, Lin Q, Cao J. Resveratrol, sirtuins, and viruses. Rev Med Virol 2015; 25:431-45. [DOI: 10.1002/rmv.1858] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 09/19/2015] [Indexed: 12/25/2022]
Affiliation(s)
- Tao Yang
- College of Food Science and Technology; Central South University of Forestry and Technology; Changsha Hunan Province China
| | - Shugang Li
- Construction Corps Key Laboratory of Deep Processing on Featured Agricultural Products in South Xinjiang; Tarim University; Alar Xinjiang China
| | - Xuming Zhang
- Department of Microbiology and Immunology; University of Arkansas for Medical Sciences; Little Rock AR USA
| | - Xiaowu Pang
- Departments of Oral Pathology, College of Dentistry; Howard University; Washington DC USA
| | - Qinlu Lin
- College of Food Science and Technology; Central South University of Forestry and Technology; Changsha Hunan Province China
| | - Jianzhong Cao
- College of Food Science and Technology; Central South University of Forestry and Technology; Changsha Hunan Province China
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Bose D, Gagnon J, Chebloune Y. Comparative Analysis of Tat-Dependent and Tat-Deficient Natural Lentiviruses. Vet Sci 2015; 2:293-348. [PMID: 29061947 PMCID: PMC5644649 DOI: 10.3390/vetsci2040293] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 08/24/2015] [Accepted: 08/24/2015] [Indexed: 01/10/2023] Open
Abstract
The emergence of human immunodeficiency virus (HIV) causing acquired immunodeficiency syndrome (AIDS) in infected humans has resulted in a global pandemic that has killed millions. HIV-1 and HIV-2 belong to the lentivirus genus of the Retroviridae family. This genus also includes viruses that infect other vertebrate animals, among them caprine arthritis-encephalitis virus (CAEV) and Maedi-Visna virus (MVV), the prototypes of a heterogeneous group of viruses known as small ruminant lentiviruses (SRLVs), affecting both goat and sheep worldwide. Despite their long host-SRLV natural history, SRLVs were never found to be responsible for immunodeficiency in contrast to primate lentiviruses. SRLVs only replicate productively in monocytes/macrophages in infected animals but not in CD4+ T cells. The focus of this review is to examine and compare the biological and pathological properties of SRLVs as prototypic Tat-independent lentiviruses with HIV-1 as prototypic Tat-dependent lentiviruses. Results from this analysis will help to improve the understanding of why and how these two prototypic lentiviruses evolved in opposite directions in term of virulence and pathogenicity. Results may also help develop new strategies based on the attenuation of SRLVs to control the highly pathogenic HIV-1 in humans.
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Affiliation(s)
- Deepanwita Bose
- Pathogénèse et Vaccination Lentivirales, PAVAL Lab., Université Joseph Fourier Grenoble 1, Bat. NanoBio2, 570 rue de la Chimie, BP 53, 38041, Grenoble Cedex 9, France.
| | - Jean Gagnon
- Pathogénèse et Vaccination Lentivirales, PAVAL Lab., Université Joseph Fourier Grenoble 1, Bat. NanoBio2, 570 rue de la Chimie, BP 53, 38041, Grenoble Cedex 9, France.
| | - Yahia Chebloune
- Pathogénèse et Vaccination Lentivirales, PAVAL Lab., Université Joseph Fourier Grenoble 1, Bat. NanoBio2, 570 rue de la Chimie, BP 53, 38041, Grenoble Cedex 9, France.
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Gao Y, Wang Y, Feng J, Feng G, Zheng M, Yang Z, Xiao Z, Lu Z, Ye L, Zhang X. A hairpin within YAP mRNA 3′UTR functions in regulation at post-transcription level. Biochem Biophys Res Commun 2015; 459:306-312. [DOI: 10.1016/j.bbrc.2015.02.106] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 02/18/2015] [Indexed: 12/26/2022]
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A mutant tat protein inhibits HIV-1 reverse transcription by targeting the reverse transcription complex. J Virol 2015; 89:4827-36. [PMID: 25673710 DOI: 10.1128/jvi.03440-14] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 02/03/2015] [Indexed: 12/24/2022] Open
Abstract
UNLABELLED Previously, we reported that a mutant of Tat referred to as Nullbasic inhibits HIV-1 reverse transcription although the mechanism of action is unknown. Here we show that Nullbasic is a reverse transcriptase (RT) binding protein that targets the reverse transcription complex rather than directly inhibiting RT activity. An interaction between Nullbasic and RT was observed by using coimmunoprecipitation and pulldown assays, and a direct interaction was measured by using a biolayer interferometry assay. Mixtures of recombinant 6×His-RT and Nullbasic-FLAG-V5-6×His at molar ratios of up to 1:20,000 did not inhibit RT activity in standard homopolymer primer template assays. An analysis of virus made by cells that coexpressed Nullbasic showed that Nullbasic copurified with virus particles, indicating that it was a virion protein. In addition, analysis of reverse transcription complexes (RTCs) isolated from cells infected with wild type or Nullbasic-treated HIV-1 showed that Nullbasic reduced the levels of viral DNA in RTC fractions. In addition, a shift in the distribution of viral DNA and CAp24 to less-dense non-RTC fractions was observed, indicating that RTC activity from Nullbasic-treated virus was impaired. Further analysis showed that viral cores isolated from Nullbasic-treated HIV undergo increased disassembly in vitro compared to untreated HIV-1. To our knowledge, this is the first description of an antiviral protein that inhibits reverse transcription by targeting the RTC and affecting core stability. IMPORTANCE HIV-1 infection is treated by using combinations of antiretroviral drugs that target independent steps of virus replication. A newly described antiviral protein called Nullbasic can also inhibit a combination of different steps in virus replication (transcription, reverse transcription, and Rev-mediated viral mRNA transport), although the precise mechanism of action is unknown. This study shows that Nullbasic can inhibit reverse transcription by binding to the viral enzyme called reverse transcriptase, which results in accelerated uncoating of the viral core and instability of the viral apparatus called the reverse transcription complex (RTC). This unique antiviral activity may inform development of other RTC inhibitors, as well as providing a unique investigative tool for dissecting the RTC cellular composition.
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Li M. Proteomics in the investigation of HIV-1 interactions with host proteins. Proteomics Clin Appl 2015; 9:221-34. [PMID: 25523935 DOI: 10.1002/prca.201400101] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 11/30/2014] [Accepted: 12/16/2014] [Indexed: 01/09/2023]
Abstract
Productive HIV-1 infection depends on host machinery, including a broad array of cellular proteins. Proteomics has played a significant role in the discovery of HIV-1 host proteins. In this review, after a brief survey of the HIV-1 host proteins that were discovered by proteomic analyses, I focus on analyzing the interactions between the virion and host proteins, as well as the technologies and strategies used in those proteomic studies. With the help of proteomics, the identification and characterization of HIV-1 host proteins can be translated into novel antiretroviral therapeutics.
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Affiliation(s)
- Ming Li
- Laboratory of Retrovirology, Division of Infectious Diseases, Department of Medicine, Alpert Medical School of Brown University, Providence, RI, USA
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Chen J, Poddar NK, Tauzin LJ, Cooper D, Kolomeisky AB, Landes CF. Single-molecule FRET studies of HIV TAR-DNA hairpin unfolding dynamics. J Phys Chem B 2014; 118:12130-9. [PMID: 25254491 PMCID: PMC4207534 DOI: 10.1021/jp507067p] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We directly measure the dynamics of the HIV trans-activation response (TAR)-DNA hairpin with multiple loops using single-molecule Förster resonance energy transfer (smFRET) methods. Multiple FRET states are identified that correspond to intermediate melting states of the hairpin. The stability of each intermediate state is calculated from the smFRET data. The results indicate that hairpin unfolding obeys a "fraying and peeling" mechanism, and evidence for the collapse of the ends of the hairpin during folding is observed. These results suggest a possible biological function for hairpin loops serving as additional fraying centers to increase unfolding rates in otherwise stable systems. The experimental and analytical approaches developed in this article provide useful tools for studying the mechanism of multistate DNA hairpin dynamics and of other general systems with multiple parallel pathways of chemical reactions.
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Affiliation(s)
- Jixin Chen
- Department of Chemistry and ‡Department of Electrical and Computer Engineering, Rice University , Houston, Texas 77251-1892, United States
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Rizzuti M, Nizzardo M, Zanetta C, Ramirez A, Corti S. Therapeutic applications of the cell-penetrating HIV-1 Tat peptide. Drug Discov Today 2014; 20:76-85. [PMID: 25277319 DOI: 10.1016/j.drudis.2014.09.017] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/11/2014] [Accepted: 09/23/2014] [Indexed: 12/29/2022]
Abstract
Over the past decades, many new therapeutic approaches have been developed for several conditions, including neurodegenerative diseases. However, efficient biodistribution and delivery at biological target sites are hampered by the presence of cell and tissue barriers, and a clinical therapy is prevented by the requirement of invasive administration routes. Candidate drug conjugation to cell-penetrating peptides, which are able to cross cellular membranes and reach biological targets even when administered systemically, represents a promising tool to overcome this issue. Here, we review the biology, classification and mechanisms of internalization of cell-penetrating peptides. We focus our attention on the cell-penetrating peptide: HIV-derived Tat peptide, and discuss its efficient but controversial use in basic, preclinical and clinical research from its discovery to the present day.
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Affiliation(s)
- Mafalda Rizzuti
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Neurology Unit, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, via Francesco Sforza 35, 20122 Milan, Italy
| | - Monica Nizzardo
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Neurology Unit, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, via Francesco Sforza 35, 20122 Milan, Italy.
| | - Chiara Zanetta
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Neurology Unit, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, via Francesco Sforza 35, 20122 Milan, Italy
| | - Agnese Ramirez
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Neurology Unit, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, via Francesco Sforza 35, 20122 Milan, Italy
| | - Stefania Corti
- Dino Ferrari Centre, Neuroscience Section, Department of Pathophysiology and Transplantation (DEPT), University of Milan, Neurology Unit, IRCCS Foundation Ca' Granda Ospedale Maggiore Policlinico, via Francesco Sforza 35, 20122 Milan, Italy
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Kellish PC, Kumar S, Mack TS, Spano MN, Hennig M, Arya DP. Multivalent Amino Sugars to Recognize Different TAR RNA Conformations. MEDCHEMCOMM 2014; 5:1235-1246. [PMID: 27076899 PMCID: PMC4828046 DOI: 10.1039/c4md00165f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Neomycin dimers synthesized using "click chemistry" with varying functionality and length in the linker region have been shown to be effective in targeting the HIV-1 TAR RNA region of the HIV virus. TAR (Transactivation Response) RNA region, a 59 base pair stem loop structure located at the 5'-end of all nascent viral transcripts interacts with its target, a key regulatory protein, Tat, and necessitates the replication of HIV-1 virus. Ethidium bromide displacement and FRET competition assays have revealed nanomolar binding affinity between neomycin dimers and wildtype TAR RNA while in case of neomycin, only a weak binding was detected. Here, NMR and FID-based comparisons reveal an extended binding interface for neomycin dimers involving the upper stem of the TAR RNA thereby offering an explanation for increased affinities. To further explore the potential of these modified aminosugars we have extended binding studies to include four TAR RNA mutants that display conformational differences with minimal sequence variation. The differences in binding between neomycin and neomycin dimers is characterized with TAR RNA mutants that include mutations to the bulge region, hairpin region, and both the bulge and hairpin regions. Our results demonstrate the effect of these mutations on neomycin binding and our results show that linker functionalities between dimeric units of neomycin can distinguish between the conformational differences of mutant TAR RNA structures.
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Affiliation(s)
- Patrick C. Kellish
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Sunil Kumar
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Todd S. Mack
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 70 President St., Charleston, SC 29425
| | | | - Mirko Hennig
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 70 President St., Charleston, SC 29425
| | - Dev P. Arya
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
- NUBAD, LLC, 900B West Faris Rd., Greenville, SC 29605
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Bouwman RD, Palser A, Parry CM, Coulter E, Rasaiyaah J, Kellam P, Jenner RG. Human immunodeficiency virus Tat associates with a specific set of cellular RNAs. Retrovirology 2014; 11:53. [PMID: 24990269 PMCID: PMC4086691 DOI: 10.1186/1742-4690-11-53] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 06/18/2014] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Human Immunodeficiency Virus 1 (HIV-1) exhibits a wide range of interactions with the host cell but whether viral proteins interact with cellular RNA is not clear. A candidate interacting factor is the trans-activator of transcription (Tat) protein. Tat is required for expression of virus genes but activates transcription through an unusual mechanism; binding to an RNA stem-loop, the transactivation response element (TAR), with the host elongation factor P-TEFb. HIV-1 Tat has also been shown to alter the expression of host genes during infection, contributing to viral pathogenesis but, whether Tat also interacts with cellular RNAs is unknown. RESULTS Using RNA immunoprecipitation coupled with microarray analysis, we have discovered that HIV-1 Tat is associated with a specific set of human mRNAs in T cells. mRNAs bound by Tat share a stem-loop structural element and encode proteins with common biological roles. In contrast, we do not find evidence that Tat associates with microRNAs or the RNA-induced silencing complex (RISC). The interaction of Tat with cellular RNA requires an intact RNA binding domain and Tat RNA binding is linked to an increase in RNA abundance in cell lines and during infection of primary CD4+ T cells by HIV. CONCLUSIONS We conclude that Tat interacts with a specific set of human mRNAs in T cells, many of which show changes in abundance in response to Tat and HIV infection. This work uncovers a previously unrecognised interaction between HIV and its host that may contribute to viral alteration of the host cellular environment.
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Affiliation(s)
| | | | | | | | | | | | - Richard G Jenner
- MRC Centre for Medical Molecular Virology, Division of Infection and Immunity, University College London, London WC1E 6BT, UK.
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Nowarski R, Prabhu P, Kenig E, Smith Y, Britan-Rosich E, Kotler M. APOBEC3G inhibits HIV-1 RNA elongation by inactivating the viral trans-activation response element. J Mol Biol 2014; 426:2840-53. [PMID: 24859335 DOI: 10.1016/j.jmb.2014.05.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 05/14/2014] [Accepted: 05/15/2014] [Indexed: 10/25/2022]
Abstract
Deamination of cytidine residues in viral DNA is a major mechanism by which APOBEC3G (A3G) inhibits vif-deficient human immunodeficiency virus type 1 (HIV-1) replication. dC-to-dU transition following RNase-H activity leads to viral cDNA degradation, production of non-functional proteins, formation of undesired stop codons and decreased viral protein synthesis. Here, we demonstrate that A3G provides an additional layer of defense against HIV-1 infection dependent on inhibition of proviral transcription. HIV-1 transcription elongation is regulated by the trans-activation response (TAR) element, a short stem-loop RNA structure required for elongation factors binding. Vif-deficient HIV-1-infected cells accumulate short viral transcripts and produce lower amounts of full-length HIV-1 transcripts due to A3G deamination of the TAR apical loop cytidine, highlighting the requirement for TAR loop integrity in HIV-1 transcription. We further show that free single-stranded DNA (ssDNA) termini are not essential for A3G activity and a gap of CCC motif blocked with juxtaposed DNA or RNA on either or 3'+5' ends is sufficient for A3G deamination. These results identify A3G as an efficient mutator and that deamination of (-)SSDNA results in an early block of HIV-1 transcription.
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Affiliation(s)
- Roni Nowarski
- Department of Pathology and Lautenberg Center for General and Tumor Immunology, Jerusalem 91120, Israel
| | - Ponnandy Prabhu
- Department of Pathology and Lautenberg Center for General and Tumor Immunology, Jerusalem 91120, Israel
| | - Edan Kenig
- Department of Pathology and Lautenberg Center for General and Tumor Immunology, Jerusalem 91120, Israel
| | - Yoav Smith
- Genomic Data Analysis Unit, The Hebrew University Hadassah Medical School, Jerusalem 91120, Israel
| | - Elena Britan-Rosich
- Department of Pathology and Lautenberg Center for General and Tumor Immunology, Jerusalem 91120, Israel
| | - Moshe Kotler
- Department of Pathology and Lautenberg Center for General and Tumor Immunology, Jerusalem 91120, Israel.
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Liu M, Li D, Sun L, Chen J, Sun X, Zhang L, Huo L, Zhou J. Modulation of Eg5 activity contributes to mitotic spindle checkpoint activation and Tat-mediated apoptosis in CD4-positive T-lymphocytes. J Pathol 2014; 233:138-47. [PMID: 24488929 DOI: 10.1002/path.4333] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Revised: 01/12/2014] [Accepted: 01/26/2014] [Indexed: 12/20/2022]
Abstract
Tat, the transactivation factor of human immunodeficiency virus type 1 (HIV-1), represents one of the major players mediating the loss of CD4-positive T-lymphocytes in HIV-1-infected patients, primarily due to the ability of Tat to trigger apoptosis. However, the molecular events underlying this process remain elusive. In this study, we provide evidence that Tat interacts with Eg5, a microtubule-associated motor protein, and allosterically modulates the ATPase activity of Eg5 by affecting ADP release from the enzyme's active centre. This action of Tat impairs the formation of the mitotic spindle and activates the spindle checkpoint, thereby blocking cell cycle progression at mitosis and leading to apoptosis. Further studies reveal that lysine 85 in the carboxyl terminus of Tat is critical for its interaction with Eg5 and hence its effects on Eg5 activity, mitotic progression, and apoptosis. These findings identify Tat as a viral regulator of Eg5 and provide novel insights into the mechanisms of action of Tat in mediating the reduction of CD4-positive T-lymphocytes.
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Affiliation(s)
- Min Liu
- Key Laboratory of Immune Microenvironment and Disease of the Ministry of Education, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
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Pagano JM, Kwak H, Waters CT, Sprouse RO, White BS, Ozer A, Szeto K, Shalloway D, Craighead HG, Lis JT. Defining NELF-E RNA binding in HIV-1 and promoter-proximal pause regions. PLoS Genet 2014; 10:e1004090. [PMID: 24453987 PMCID: PMC3894171 DOI: 10.1371/journal.pgen.1004090] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 11/22/2013] [Indexed: 11/22/2022] Open
Abstract
The four-subunit Negative Elongation Factor (NELF) is a major regulator of RNA Polymerase II (Pol II) pausing. The subunit NELF-E contains a conserved RNA Recognition Motif (RRM) and is proposed to facilitate Poll II pausing through its association with nascent transcribed RNA. However, conflicting ideas have emerged for the function of its RNA binding activity. Here, we use in vitro selection strategies and quantitative biochemistry to identify and characterize the consensus NELF-E binding element (NBE) that is required for sequence specific RNA recognition (NBE: CUGAGGA(U) for Drosophila). An NBE-like element is present within the loop region of the transactivation-response element (TAR) of HIV-1 RNA, a known regulatory target of human NELF-E. The NBE is required for high affinity binding, as opposed to the lower stem of TAR, as previously claimed. We also identify a non-conserved region within the RRM that contributes to the RNA recognition of Drosophila NELF-E. To understand the broader functional relevance of NBEs, we analyzed promoter-proximal regions genome-wide in Drosophila and show that the NBE is enriched +20 to +30 nucleotides downstream of the transcription start site. Consistent with the role of NELF in pausing, we observe a significant increase in NBEs among paused genes compared to non-paused genes. In addition to these observations, SELEX with nuclear run-on RNA enrich for NBE-like sequences. Together, these results describe the RNA binding behavior of NELF-E and supports a biological role for NELF-E in promoter-proximal pausing of both HIV-1 and cellular genes. RNA polymerase II (Pol II) is a molecular machine that is responsible for transcribing all protein coding genes in the eukaryotic genome. Transcription by Pol II is a highly regulated process consisting of several rate-limiting steps. During transcription elongation, a number of transcription factors are essential to modulate Pol II activity. One of these factors is the Negative Elongation Factor (NELF), and it plays a major role in promoter-proximal pausing, a widespread phenomenon during early transcription elongation. NELF-E, a protein subunit of the NELF complex contains a conserved RNA binding domain that is thought to regulate transcription through its interaction with newly transcribed RNA made by Pol II. However, the function of the RNA binding activity of NELF-E remains unresolved due to prior conflicting studies. Here, we clarify the RNA binding properties of NELF-E and provide insight into how this protein might facilitate promoter-proximal pausing of Pol II in transcription. Moreover, we identify the precise region of NELF-E binding in one of its known regulatory targets, HIV-1. Taken together, the results presented indicate a dynamic interplay between NELF and specific RNA sequences around the promoter pause region to modulate early transcription elongation.
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Affiliation(s)
- John M Pagano
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Hojoong Kwak
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Colin T Waters
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Rebekka O Sprouse
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Brian S White
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri, United States of America
| | - Abdullah Ozer
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Kylan Szeto
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York, United States of America
| | - David Shalloway
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Harold G Craighead
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York, United States of America
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
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Joly JP, Mata G, Eldin P, Briant L, Fontaine-Vive F, Duca M, Benhida R. Artificial Nucleobase-Amino Acid Conjugates: A New Class of TAR RNA Binding Agents. Chemistry 2014; 20:2071-9. [DOI: 10.1002/chem.201303664] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Indexed: 12/23/2022]
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50
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Bagashev A, Sawaya BE. Roles and functions of HIV-1 Tat protein in the CNS: an overview. Virol J 2013; 10:358. [PMID: 24359561 PMCID: PMC3879180 DOI: 10.1186/1743-422x-10-358] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 12/06/2013] [Indexed: 01/01/2023] Open
Abstract
Nearly 50% of HIV-infected individuals suffer from some form of HIV-associated neurocognitive disorders (HAND). HIV-1 Tat (a key HIV transactivator of transcription) protein is one of the first HIV proteins to be expressed after infection occurs and is absolutely required for the initiation of the HIV genome transcription. In addition to its canonical functions, various studies have shown the deleterious role of HIV-1 Tat in the development and progression of HAND. Within the CNS, only specific cell types can support productive viral replication (astrocytes and microglia), however Tat protein can be released form infected cells to affects HIV non-permissive cells such as neurons. Therefore, in this review, we will summarize the functions of HIV-1 Tat proteins in neural cells and its ability to promote HAND.
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Affiliation(s)
| | - Bassel E Sawaya
- Molecular Studies of Neurodegenerative Diseases Lab, The Fels Institute for Cancer Research & Molecular Biology, Philadelphia, PA 19140, USA.
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