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Geng A, Ganser L, Roy R, Shi H, Pratihar S, Case DA, Al-Hashimi HM. An RNA excited conformational state at atomic resolution. Nat Commun 2023; 14:8432. [PMID: 38114465 PMCID: PMC10730710 DOI: 10.1038/s41467-023-43673-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 11/16/2023] [Indexed: 12/21/2023] Open
Abstract
Sparse and short-lived excited RNA conformational states are essential players in cell physiology, disease, and therapeutic development, yet determining their 3D structures remains challenging. Combining mutagenesis, NMR spectroscopy, and computational modeling, we determined the 3D structural ensemble formed by a short-lived (lifetime ~2.1 ms) lowly-populated (~0.4%) conformational state in HIV-1 TAR RNA. Through a strand register shift, the excited conformational state completely remodels the 3D structure of the ground state (RMSD from the ground state = 7.2 ± 0.9 Å), forming a surprisingly more ordered conformational ensemble rich in non-canonical mismatches. The structure impedes the formation of the motifs recognized by Tat and the super elongation complex, explaining why this alternative TAR conformation cannot activate HIV-1 transcription. The ability to determine the 3D structures of fleeting RNA states using the presented methodology holds great promise for our understanding of RNA biology, disease mechanisms, and the development of RNA-targeting therapeutics.
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Affiliation(s)
- Ainan Geng
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Laura Ganser
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Rohit Roy
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, NC, 27708, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA
| | - Supriya Pratihar
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - David A Case
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA.
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2
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Roy R, Geng A, Shi H, Merriman DK, Dethoff EA, Salmon L, Al-Hashimi HM. Kinetic Resolution of the Atomic 3D Structures Formed by Ground and Excited Conformational States in an RNA Dynamic Ensemble. J Am Chem Soc 2023; 145:22964-22978. [PMID: 37831584 DOI: 10.1021/jacs.3c04614] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
Knowing the 3D structures formed by the various conformations populating the RNA free-energy landscape, their relative abundance, and kinetic interconversion rates is required to obtain a quantitative and predictive understanding of how RNAs fold and function at the atomic level. While methods integrating ensemble-averaged experimental data with computational modeling are helping define the most abundant conformations in RNA ensembles, elucidating their kinetic rates of interconversion and determining the 3D structures of sparsely populated short-lived RNA excited conformational states (ESs) remains challenging. Here, we developed an approach integrating Rosetta-FARFAR RNA structure prediction with NMR residual dipolar couplings and relaxation dispersion that simultaneously determines the 3D structures formed by the ground-state (GS) and ES subensembles, their relative abundance, and kinetic rates of interconversion. The approach is demonstrated on HIV-1 TAR, whose six-nucleotide apical loop was previously shown to form a sparsely populated (∼13%) short-lived (lifetime ∼ 45 μs) ES. In the GS, the apical loop forms a broad distribution of open conformations interconverting on the pico-to-nanosecond time scale. Most residues are unpaired and preorganized to bind the Tat-superelongation protein complex. The apical loop zips up in the ES, forming a narrow distribution of closed conformations, which sequester critical residues required for protein recognition. Our work introduces an approach for determining the 3D ensemble models formed by sparsely populated RNA conformational states, provides a rare atomic view of an RNA ES, and kinetically resolves the atomic 3D structures of RNA conformational substates, interchanging on time scales spanning 6 orders of magnitude, from picoseconds to microseconds.
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Affiliation(s)
- Rohit Roy
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Ainan Geng
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, United States
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Dawn K Merriman
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Elizabeth A Dethoff
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Loïc Salmon
- Department of Chemistry and Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hashim M Al-Hashimi
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, United States
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3
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Guo X, Tang T, Duan M, Zhang L, Ge H. The nonequilibrium mechanism of noise-enhanced drug synergy in HIV latency reactivation. iScience 2022; 25:104358. [PMID: 35620426 PMCID: PMC9127169 DOI: 10.1016/j.isci.2022.104358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 03/04/2022] [Accepted: 04/29/2022] [Indexed: 11/29/2022] Open
Abstract
Noise-modulating chemicals can synergize with transcriptional activators in reactivating latent HIV to eliminate latent HIV reservoirs. To understand the underlying biomolecular mechanism, we investigate a previous two-gene-state model and identify two necessary conditions for the synergy: an assumption of the inhibition effect of transcription activators on noise enhancers; and frequent transitions to the gene non-transcription-permissive state. We then develop a loop-four-gene-state model with Tat transcription/translation and find that drug synergy is mainly determined by the magnitude and direction of energy input into the genetic regulatory kinetics of the HIV promoter. The inhibition effect of transcription activators is actually a phenomenon of energy dissipation in the nonequilibrium gene transition system. Overall, the loop-four-state model demonstrates that energy dissipation plays a crucial role in HIV latency reactivation, which might be useful for improving drug effects and identifying other synergies on lentivirus latency reactivation. The inhibition of Activator on Noise enhancer is necessary for their synergy in reactivating HIV The drug synergy is a nonequilibrium phenomenon in the gene regulatory system The magnitude and direction of energy input determine the drug synergy This nonequilibrium mechanism is general without regarding molecular details
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4
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Ganser LR, Kelly ML, Patwardhan NN, Hargrove AE, Al-Hashimi HM. Demonstration that Small Molecules can Bind and Stabilize Low-abundance Short-lived RNA Excited Conformational States. J Mol Biol 2019; 432:1297-1304. [PMID: 31863746 DOI: 10.1016/j.jmb.2019.12.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 11/23/2019] [Accepted: 12/04/2019] [Indexed: 11/26/2022]
Abstract
Many promising RNA drug targets have functions that require the formation of RNA-protein complexes, but inhibiting RNA-protein interactions can prove difficult using small molecules. Regulatory RNAs have been shown to transiently form excited conformational states (ESs) that remodel local aspects of secondary structure. In some cases, the ES conformation has been shown to be inactive and to be poorly recognized by protein binding partners. In these cases, specifically targeting and stabilizing the RNA ES using a small molecule provides a rational structure-based strategy for inhibiting RNA activity. However, this requires that a small molecule discriminates between two conformations of the same RNA to preferentially bind and stabilize the short-lived low-abundance ES relative to the long-lived more abundant ground state (GS). Here, we tested the feasibility of this approach by designing a mutant that inverts the conformational equilibrium of the HIV-1 transactivation response element (TAR) RNA, such that the native GS conformation becomes a low-abundance ES. Using this mutant and NMR chemical shift mapping experiments, we show that argininamide, a ligand mimic of TAR's cognate protein binding partner Tat, is able to restore a native-like conformation by preferentially binding and stabilizing the transient and low-populated ES. A synthetic small molecule optimized to bind the TAR GS also partially stabilized the ES, whereas an aminoglycoside molecule that binds RNAs nonspecifically did not preferentially stabilize the ES to a similar extent. These results support the feasibility of inhibiting RNA activity using small molecules that preferentially bind and stabilize the ES.
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Affiliation(s)
- Laura R Ganser
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, USA
| | - Megan L Kelly
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, USA
| | | | - Amanda E Hargrove
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, USA; Department of Chemistry, Duke University, Durham, NC, 27708, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710, USA.
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5
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Taherpour S, Lönnberg T. Fluorescence probing of metal-ion-mediated hybridization of oligonucleotides. RSC Adv 2015. [DOI: 10.1039/c4ra15136d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The structure-dependent fluorescence of pyrrolocytosine has been harnessed to quantify the affinity of metal-ion-chelating oligonucleotides for their native counterparts.
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6
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Musiani F, Rossetti G, Capece L, Gerger TM, Micheletti C, Varani G, Carloni P. Molecular dynamics simulations identify time scale of conformational changes responsible for conformational selection in molecular recognition of HIV-1 transactivation responsive RNA. J Am Chem Soc 2014; 136:15631-7. [PMID: 25313638 PMCID: PMC5521259 DOI: 10.1021/ja507812v] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The HIV-1 Tat protein and several small molecules bind to HIV-1 transactivation responsive RNA (TAR) by selecting sparsely populated but pre-existing conformations. Thus, a complete characterization of TAR conformational ensemble and dynamics is crucial to understand this paradigmatic system and could facilitate the discovery of new antivirals targeting this essential regulatory element. We show here that molecular dynamics simulations can be effectively used toward this goal by bridging the gap between functionally relevant time scales that are inaccessible to current experimental techniques. Specifically, we have performed several independent microsecond long molecular simulations of TAR based on one of the most advanced force fields available for RNA, the parmbsc0 AMBER. Our simulations are first validated against available experimental data, yielding an excellent agreement with measured residual dipolar couplings and order parameter S(2). This contrast with previous molecular dynamics simulations (Salmon et al., J. Am. Chem. Soc. 2013 135, 5457-5466) based on the CHARMM36 force field, which could achieve only modest accord with the experimental RDC values. Next, we direct the computation toward characterizing the internal dynamics of TAR over the microsecond time scale. We show that the conformational fluctuations observed over this previously elusive time scale have a strong functionally oriented character in that they are primed to sustain and assist ligand binding.
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Affiliation(s)
- Francesco Musiani
- Scuola Internazionale Superiore di Studi Avanzati (SISSA/ISAS), via Bonomea 265, 34136 Trieste, Italy
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, 40127 Bologna, Italy
- Institute of Neuroscience and Medicine INM-9 and Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Computational Biophysics, German Research School for Simulation Sciences, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Giulia Rossetti
- Institute of Neuroscience and Medicine INM-9 and Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Computational Biophysics, German Research School for Simulation Sciences, Forschungszentrum Jülich, 52425 Jülich, Germany
- Jülich Supercomputing Centre, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Luciana Capece
- International Centre for Genetic Engineering and Biotechnology, AREA Science Park, Padriciano 99, 34149 Trieste, Italy
| | - Thomas Martin Gerger
- Institute of Neuroscience and Medicine INM-9 and Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Computational Biophysics, German Research School for Simulation Sciences, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Cristian Micheletti
- Scuola Internazionale Superiore di Studi Avanzati (SISSA/ISAS), via Bonomea 265, 34136 Trieste, Italy
| | - Gabriele Varani
- Department of Chemistry and Department of Biochemistry, University of Washington, Seattle, 98195 WA, USA
| | - Paolo Carloni
- Institute of Neuroscience and Medicine INM-9 and Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Computational Biophysics, German Research School for Simulation Sciences, Forschungszentrum Jülich, 52425 Jülich, Germany
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7
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van Bracht E, Versteegden LRM, Stolle S, Verdurmen WPR, Woestenenk R, Raavé R, Hafmans T, Oosterwijk E, Brock R, van Kuppevelt TH, Daamen WF. Enhanced cellular uptake of albumin-based lyophilisomes when functionalized with cell-penetrating peptide TAT in HeLa cells. PLoS One 2014; 9:e110813. [PMID: 25369131 PMCID: PMC4219704 DOI: 10.1371/journal.pone.0110813] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 09/23/2014] [Indexed: 01/24/2023] Open
Abstract
Lyophilisomes are a novel class of biodegradable proteinaceous nano/micrometer capsules with potential use as drug delivery carrier. Cell-penetrating peptides (CPPs) including the TAT peptide have been successfully implemented for intracellular delivery of a broad variety of cargos including various nanoparticulate pharmaceutical carriers. In the present study, lyophilisomes were modified using CPPs in order to achieve enhanced cellular uptake. Lyophilisomes were prepared by a freezing, annealing, and lyophilization method and a cystein-elongated TAT peptide was conjugated to the lyophilisomes using a heterobifunctional linker. Fluorescent-activated cell sorting (FACS) was utilized to acquire a lyophilisome population with a particle diameter smaller than 1000 nm. Cultured HeLa, OVCAR-3, Caco-2 and SKOV-3 cells were exposed to unmodified lyophilisomes and TAT-conjugated lyophilisomes and examined with FACS. HeLa cells were investigated in more detail using a trypan blue quenching assay, confocal microscopy, and transmission electron microscopy. TAT-conjugation strongly increased binding and cellular uptake of lyophilisomes in a time-dependent manner in vitro, as assessed by FACS. These results were confirmed by confocal microscopy. Transmission electron microscopy indicated rapid cellular uptake of TAT-conjugated lyophilisomes via phagocytosis and/or macropinocytosis. In conclusion, TAT-peptides conjugated to albumin-based lyophilisomes are able to enhance cellular uptake of lyophilisomes in HeLa cells.
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Affiliation(s)
- Etienne van Bracht
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud university medical centre, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Luuk R. M. Versteegden
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud university medical centre, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Sarah Stolle
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud university medical centre, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Wouter P. R. Verdurmen
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud university medical centre, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Rob Woestenenk
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud university medical centre, Geert Grooteplein 8, 6525 GA, Nijmegen, The Netherlands
| | - René Raavé
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud university medical centre, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Theo Hafmans
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud university medical centre, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Egbert Oosterwijk
- Department of Urology, Radboud Institute for Molecular Life Sciences, Radboud university medical centre, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Roland Brock
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud university medical centre, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Toin H. van Kuppevelt
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud university medical centre, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
| | - Willeke F. Daamen
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud university medical centre, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands
- * E-mail:
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Samikkannu T, Rao KVK, Kanthikeel SP, Atluri VSR, Agudelo M, Roy U, Nair MPN. Immunoneuropathogenesis of HIV-1 clades B and C: role of redox expression and thiol modification. Free Radic Biol Med 2014; 69:136-44. [PMID: 24480751 PMCID: PMC4211896 DOI: 10.1016/j.freeradbiomed.2013.12.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 12/19/2013] [Accepted: 12/22/2013] [Indexed: 12/23/2022]
Abstract
Previous studies have shown that, during infection, HIV-1 clade B and clade C differentially contribute to the neuropathogenesis and development of HIV-associated neurocognitive disorders (HANDs). The low-molecular-weight tripeptide glutathione (GSH) alters the redox balance and leads to the generation of reactive oxygen species, which play a significant role in the neuropathogenesis of HANDs. We hypothesized that the HIV-1 clade B and clade C viruses and their respective Tat proteins exert differential effects on monocyte-derived immature dendritic cells (IDCs) and neuroblastoma cells (SK-N-MC) by redox activation, which leads to immunoneuropathogenesis. The GSH/GSSG ratio and mRNA expression levels and protein modification of glutathione synthetase (GSS), glutathione peroxidase 1 (GPx1), superoxide dismutase 1 (SOD1), and catalase (CAT) were analyzed in IDCs infected with HIV-1 clade B or clade C as well as in cells treated with the respective Tat proteins. The results indicated that HIV-1 clade B virus and its Tat protein significantly increased the production of reactive oxygen species and reduced the GSH/GSSG ratio and subsequent downregulation of gene expression and protein modification of GSS, GPx1, SOD1, and CAT compared to infection with the clade C virus or treatment with the clade C Tat protein. Thus, our studies demonstrate that HIV-1 clades B and C exert differential effects of redox expression and thiol modification. HIV-1 clade B potentially induces oxidative stress, leading to more immunoneuropathogenesis than infection with HIV-1 clade C.
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Affiliation(s)
- Thangavel Samikkannu
- Department of Immunology, Institute of NeuroImmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Kurapati V K Rao
- Department of Immunology, Institute of NeuroImmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Sudhessh Pilakka Kanthikeel
- Department of Immunology, Institute of NeuroImmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Venkata Subba Rao Atluri
- Department of Immunology, Institute of NeuroImmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Marisela Agudelo
- Department of Immunology, Institute of NeuroImmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Upal Roy
- Department of Immunology, Institute of NeuroImmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Madhavan P N Nair
- Department of Immunology, Institute of NeuroImmune Pharmacology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA.
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Yin J, Zhu D, Zhang Z, Wang W, Fan J, Men D, Deng J, Wei H, Zhang XE, Cui Z. Imaging of mRNA-protein interactions in live cells using novel mCherry trimolecular fluorescence complementation systems. PLoS One 2013; 8:e80851. [PMID: 24260494 PMCID: PMC3829953 DOI: 10.1371/journal.pone.0080851] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2013] [Accepted: 10/15/2013] [Indexed: 11/18/2022] Open
Abstract
Live cell imaging of mRNA-protein interactions makes it possible to study posttranscriptional processes of cellular and viral gene expression under physiological conditions. In this study, red color mCherry-based trimolecular fluorescence complementation (TriFC) systems were constructed as new tools for visualizing mRNA-protein interaction in living cells using split mCherry fragments and HIV REV-RRE and TAT-TAR peptide-RNA interaction pairs. The new mCherry TriFC systems were successfully used to image RNA-protein interactions such as that between influenza viral protein NS1 and the 5' UTR of influenza viral mRNAs NS, M, and NP. Upon combination of an mCherry TriFC system with a Venus TriFC system, multiple mRNA-protein interactions could be detected simultaneously in the same cells. Then, the new mCherry TriFC system was used for imaging of interactions between influenza A virus mRNAs and some of adapter proteins in cellular TAP nuclear export pathway in live cells. Adapter proteins Aly and UAP56 were found to associate with three kinds of viral mRNAs. Another adapter protein, splicing factor 9G8, only interacted with intron-containing spliced M2 mRNA. Co-immunoprecipitation assays with influenza A virus-infected cells confirmed these interactions. This study provides long-wavelength-spectrum TriFC systems as new tools for visualizing RNA-protein interactions in live cells and help to understand the nuclear export mechanism of influenza A viral mRNAs.
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Affiliation(s)
- Juan Yin
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Duanhao Zhu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Zhiping Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Wei Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Jinyu Fan
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Dong Men
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Jiaoyu Deng
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Hongping Wei
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Xian-En Zhang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Zongqiang Cui
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
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10
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Ben Haij N, Leghmari K, Planès R, Thieblemont N, Bahraoui E. HIV-1 Tat protein binds to TLR4-MD2 and signals to induce TNF-α and IL-10. Retrovirology 2013; 10:123. [PMID: 24165011 PMCID: PMC4231456 DOI: 10.1186/1742-4690-10-123] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 10/09/2013] [Indexed: 12/19/2022] Open
Abstract
Background HIV-1 infection results in hyper-immune activation and immunological disorders as early as the asymptomatic stage. Here, we hypothesized that during early HIV-1 infection, HIV-1 Tat protein acts on monocytes/macrophages to induce anti-inflammatory and proinflammatory cytokines and participates in immune dysregulation. Results In this work we showed that Tat protein: i) by its N-terminal domain induces production of both IL-10 and TNF-α in a TLR4-MD2 dependent manner, ii) interacts specifically with TLR4-MD2 and MD2 with high affinity but not with CD14, iii) induces in vivo TNF-α and IL-10 in a TLR4 dependent manner. Conclusions Collectively, our data showed for the first time that, HIV-1 Tat interacts physically with high affinity with TLR4-MD2 to promote proinflammatory cytokines (TNF-α) and the immunosuppressive cytokine IL-10 both involved in immune dysregulation during early HIV-1 infection and AIDS progression.
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Affiliation(s)
- Nawal Ben Haij
- Université Paul Sabatier, EA 3038, 118 Route de Narbonne, 31062 Toulouse, France.
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11
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Planès R, Bahraoui E. HIV-1 Tat protein induces the production of IDO in human monocyte derived-dendritic cells through a direct mechanism: effect on T cells proliferation. PLoS One 2013; 8:e74551. [PMID: 24073214 PMCID: PMC3779232 DOI: 10.1371/journal.pone.0074551] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 08/02/2013] [Indexed: 12/21/2022] Open
Abstract
During HIV-1 infection, an increase of indoleamine 2,3 dioxygenase (IDO) expression, and dendritic cells (DC) dysfunction were often associated with AIDS disease progression. In this work, we investigated the effect of HIV-1 Tat protein on the expression of IDO, in MoDCs. We show that Tat induces IDO protein expression and activity in a dose dependent manner by acting at the cell membrane. Using Tat-mutants, we show that the N-Terminal domain, Tat 1–45, but not the central region, Tat 30–72, is sufficient to induce the expression of active IDO. Tat protein is also able to induce several cytokines in MoDCs, including IFN-γ, a strong inducer of IDO. In order to understand whether IDO is induced directly by Tat protein or indirectly following IFN-γ production, complementary experiments were performed and showed that: i) at the kinetic level, Tat induced IDO expression before the production of IFN-γ ii) treatment of MoDCs with Tat-conditioned medium was unable to stimulate IDO expression, iii) coculture of MoDCs in a transwell cell system did not allow IDO expression in MoDCs not previously treated by Tat, iv) direct contact between Tat-treated and untreated MoDCs was not sufficient to induce IDO expression in a Tat-independent manner, and v) treatment of MoDCs in the presence of IFN-γ pathway inhibitors, Jak I and Ly294002, inhibited IFN-γ-induced IDO but had no effect on Tat-induced IDO. At the functional level, our data showed that treatment of MoDCs with Tat led to the inhibition of their capacity to stimulate T cell proliferation. This impairement was totally abolished when the stimulation was performed in the presence of 1MT, an inhibitor of IDO activity, arguing for the implication of the kynurenine pathway. By inducing IDO, Tat protein may be considered, as a viral pathogenic factor, in the dysregulation of the DC functions during HIV-1 infection.
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Affiliation(s)
- Rémi Planès
- INSERM, U1043, Toulouse, France
- CNRS, U5282, Toulouse, France
- Université Paul Sabatier, EA 3038, Toulouse, France
| | - Elmostafa Bahraoui
- INSERM, U1043, Toulouse, France
- CNRS, U5282, Toulouse, France
- Université Paul Sabatier, EA 3038, Toulouse, France
- * E-mail:
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12
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Kumar S, Arya DP. Recognition of HIV TAR RNA by triazole linked neomycin dimers. Bioorg Med Chem Lett 2011; 21:4788-92. [PMID: 21757341 PMCID: PMC3673547 DOI: 10.1016/j.bmcl.2011.06.058] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 06/10/2011] [Accepted: 06/13/2011] [Indexed: 10/18/2022]
Abstract
A series of neomycin dimers have been synthesized using 'click chemistry' with varying linker functionality and length to target the TAR RNA region of HIV virus. TAR (trans activation response) RNA region, a 59 base pair stem loop structure located at 5'-end of all nascent HIV-1 transcripts interacts with a key regulatory protein, Tat, and necessitates the replication of HIV-1 virus. Neomycin, an aminosugar, has been shown to exhibit more than one binding site with HIV TAR RNA. Multiple TAR binding sites of neomycin prompted us to design and synthesize a small library of neomycin dimers using click chemistry. The binding between neomycin dimers and HIV TAR RNA was characterized using spectroscopic techniques including FID (Fluorescent Intercalator Displacement) titration and UV-thermal denaturation. UV thermal denaturation studies demonstrate that neomycin dimer binding increase the melting temperature (T(m)) of the HIV TAR RNA up to 10°C. Ethidium bromide displacement titrations revealed nanomolar IC(50) between neomycin dimers and HIV TAR RNA, whereas with neomycin, a much higher IC(50) in the micromolar range is observed.
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Affiliation(s)
- Sunil Kumar
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, United States
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13
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Asare-Okai PN, Chow CS. A modified fluorescent intercalator displacement assay for RNA ligand discovery. Anal Biochem 2011; 408:269-76. [PMID: 20863807 PMCID: PMC2980581 DOI: 10.1016/j.ab.2010.09.020] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 09/13/2010] [Indexed: 11/21/2022]
Abstract
Fluorescent intercalator displacement (FID) is a convenient and practical tool for identifying new nucleic acid-binding ligands. The success of FID is based on the fact that it can be fashioned into a versatile screening assay for assessing the relative binding affinities of compounds to nucleic acids. FID is a tagless approach; the target RNAs and the ligands or small molecules under investigation do not need to be modified in order to be examined. In this study, a modified FID assay for screening RNA-binding ligands was established using 3-methyl-2-((1-(3-(trimethylammonio)propyl)-4-quinolinylidene)methyl)benzothiazolium (TO-PRO) as the fluorescent indicator. Electrospray ionization mass spectrometry (ESI-MS) results provide direct evidence that correlates the reduction in fluorescence intensity observed in the FID assay with displacement of the dye molecule from RNA. The assay was successfully applied to screen a variety of RNA-binding ligands with a set of small hairpin RNAs. Ligands that bind with moderate affinity to the chosen RNA constructs (A-site, TAR [transactivation response element], h31 [helix 31], and H69 [helix 69] were identified.
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14
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Razooky BS, Weinberger LS. Mapping the architecture of the HIV-1 Tat circuit: A decision-making circuit that lacks bistability and exploits stochastic noise. Methods 2011; 53:68-77. [PMID: 21167940 PMCID: PMC4096296 DOI: 10.1016/j.ymeth.2010.12.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2010] [Indexed: 01/02/2023] Open
Abstract
Upon infection of a CD4(+) T cell, HIV-1 appears to 'choose' between two alternate fates: active replication or a long-lived dormant state termed proviral latency. A transcriptional positive-feedback loop generated by the HIV-1 Tat protein appears sufficient to mediate this decision. Here, we describe a coupled wet-lab and computational approach that uses mathematical modeling and live-cell time-lapse microscopy to map the architecture of the HIV-1 Tat transcriptional regulatory circuit and generate predictive models of HIV-1 latency. This approach provided the first characterization of a 'decision-making' circuit that lacks bistability and instead exploits stochastic fluctuations in cellular molecules (i.e. noise) to generate a decision between an on or off transcriptional state.
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Affiliation(s)
- Brandon S. Razooky
- Department of Chemistry and Biochemistry, U niversity of California, San Diego 9500 Gilman Drive #0314, La Jolla, CA 92093-0314
| | - Leor S. Weinberger
- Department of Chemistry and Biochemistry, U niversity of California, San Diego 9500 Gilman Drive #0314, La Jolla, CA 92093-0314
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15
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Bonnard V, Pascale L, Azoulay S, Di Giorgio A, Rogez-Kreuz C, Storck K, Clayette P, Patino N. Polyamide Amino Acids trimers as TAR RNA ligands and anti-HIV agents. Bioorg Med Chem 2010; 18:7432-8. [DOI: 10.1016/j.bmc.2010.09.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Revised: 08/30/2010] [Accepted: 09/01/2010] [Indexed: 10/19/2022]
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16
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Saribas AS, Ozdemir A, Lam C, Safak M. JC virus-induced Progressive Multifocal Leukoencephalopathy. Future Virol 2010; 5:313-323. [PMID: 21731577 PMCID: PMC3128336 DOI: 10.2217/fvl.10.12] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Progressive multifocal encephalopathy (PML) is a fatal demyelinating disease of the central nervous system (CNS), caused by the lytic infection of oligodendrocytes by a human polyomavirus, JC virus (JCV). PML is rare disease but mostly develops in patients with underlying immunosuppressive conditions, including Hodgkin's lymphoma, lymphoproliferative diseases, in those undergoing antineoplastic therapy and AIDS. However, consistent with the occurrence of PML under immunocompromised conditions, this disease seems to be also steadily increasing among autoimmune disease patients (multiple sclerosis and Crohn's disease), who are treated with antibody-based regimens (natalizumab, efalizumab and rituximab). This unexpected occurrence of the disease among such a patient population reconfirms the existence of a strong link between the underlying immunosuppressive conditions and development of PML. These recent observations have generated a new interest among investigators to further examine the unique biology of JCV.
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Affiliation(s)
- A Sami Saribas
- Department of Neuroscience and Center for Neurovirology, Temple University School of Medicine, Education & Research Building (MERB-757), 3500 North Broad Street-7th floor, Philadelphia, PA 19140-5104
| | - Ahmet Ozdemir
- Department of Neuroscience and Center for Neurovirology, Temple University School of Medicine, Education & Research Building (MERB-757), 3500 North Broad Street-7th floor, Philadelphia, PA 19140-5104
| | - Cathy Lam
- Department of Neuroscience and Center for Neurovirology, Temple University School of Medicine, Education & Research Building (MERB-757), 3500 North Broad Street-7th floor, Philadelphia, PA 19140-5104
| | - Mahmut Safak
- Department of Neuroscience and Center for Neurovirology, Temple University School of Medicine, Education & Research Building (MERB-757), 3500 North Broad Street-7th floor, Philadelphia, PA 19140-5104
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17
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Zhang X, Cekan P, Sigurdsson ST, Qin PZ. Studying RNA using site-directed spin-labeling and continuous-wave electron paramagnetic resonance spectroscopy. Methods Enzymol 2009; 469:303-28. [PMID: 20946796 DOI: 10.1016/s0076-6879(09)69015-7] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
In site-directed spin-labeling (SDSL), a stable nitroxide radical is attached to a specific location within a macromolecule and electron paramagnetic resonance (EPR) spectroscopy is used to interrogate the local environment surrounding the nitroxide. The SDSL strategy enables probing site-specific structural and dynamic features of RNA in solution without being limited by the size of the molecule, thus serving as a unique tool in biophysical studies of RNA. This chapter describes the use of continuous-wave (cw)-EPR to study dynamic features of RNAs as well as to monitor interactions between them. Various approaches for attaching nitroxide spin labels to nucleic acids are described, followed by detailed descriptions of cw-EPR spectral acquisition and processing procedures. Specific examples are subsequently used to illustrate analysis of EPR spectra, showing how information regarding the parent RNA can be extracted.
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Affiliation(s)
- Xiaojun Zhang
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
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18
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19
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Setiyaningsih S, Desport M, Stewart ME, Hartaningsih N, Wilcox GE. Sequence analysis of mRNA transcripts encoding Jembrana disease virus Tat-1 in vivo. Virus Res 2008; 132:220-5. [DOI: 10.1016/j.virusres.2007.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2007] [Revised: 11/07/2007] [Accepted: 11/08/2007] [Indexed: 10/22/2022]
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20
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Zhou J, Wang G, Zhang LH, Ye XS. Modifications of aminoglycoside antibiotics targeting RNA. Med Res Rev 2007; 27:279-316. [PMID: 16892199 DOI: 10.1002/med.20085] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The increased awareness of the central role of RNA has led to realization that RNA, as structural and functional information accumulation, is also drug target to small molecular therapy. Aminoglycosides are a group of well-known antibiotics, which function through binding to specific sites in prokaryotic ribosomal RNA (rRNA) and affecting the fidelity of protein synthesis. Unfortunately, their clinical practice has been curtailed by toxicity and rapid increasing number of resistant strains. Therefore, it is highly desirable to design new modified aminoglycosides that will overcome the undesirable properties of natural occurring aminoglycosides. On the other hand, aminoglycosides as potential antiviral (HIV) agents were also reported. Herein, we survey the current efforts to develop new aminoglycoside derivatives with modification and reconstruction on each sugar ring and review the latest advances in structure-activity relationships (SAR).
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Affiliation(s)
- Jian Zhou
- The State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100083, China
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21
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Raghunathan D, Sánchez-Pedregal VM, Junker J, Schwiegk C, Kalesse M, Kirschning A, Carlomagno T. TAR-RNA recognition by a novel cyclic aminoglycoside analogue. Nucleic Acids Res 2006; 34:3599-608. [PMID: 16855296 PMCID: PMC1524922 DOI: 10.1093/nar/gkl494] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The formation of the Tat-protein/TAR-RNA complex is a crucial step in the regulation of human immunodeficiency virus (HIV)-gene expression. To obtain full-length viral transcripts the Tat/TAR complex has to recruit the positive transcription elongation factor complex (P-EFTb), which interacts with TAR through its cyclin T1 (CycT1) component. Mutational studies identified the TAR hexanucleotide loop as a crucial region for contacting CycT1. Interfering with the interaction between the Tat/CycT1 complex and the TAR-RNA is an attractive strategy for the design of anti-HIV drugs. Positively charged molecules, like aminoglycosides or peptidomimetics, bind the TAR-RNA, disrupting the Tat/TAR complex. Here, we investigate the complex between the HIV-2 TAR-RNA and a neooligoaminodeoxysaccharide by NMR spectroscopy. In contrast to other aminoglycosides, this novel aminoglycoside analogue contacts simultaneously the bulge residues required for Tat binding and the A35 residue of the hexanucleotide loop. Upon complex formation, the loop region undergoes profound conformational changes. The novel binding mode, together with the easy accessibility of derivatives for the neooligoaminodeoxysaccharide, could open the way to the design of a new class of TAR-RNA binders, which simultaneously inhibit the formation of both the Tat/TAR binary complex and the Tat/TAR/CycT1 ternary complex by obstructing both the bulge and loop regions of the RNA.
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Affiliation(s)
| | | | | | | | - Markus Kalesse
- Institute of Organic Chemistry, University of HannoverSchneiderberg 1B, D-30167 Hannover, Germany
| | - Andreas Kirschning
- Institute of Organic Chemistry, University of HannoverSchneiderberg 1B, D-30167 Hannover, Germany
| | - Teresa Carlomagno
- To whom correspondence should be addressed. Tel: +49 551 201 2214; Fax: +49 551 201 2202;
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22
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Edwards TE, Robinson BH, Sigurdsson ST. Identification of amino acids that promote specific and rigid TAR RNA-tat protein complex formation. ACTA ACUST UNITED AC 2005; 12:329-37. [PMID: 15797217 DOI: 10.1016/j.chembiol.2005.01.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2004] [Revised: 01/19/2005] [Accepted: 01/20/2005] [Indexed: 11/28/2022]
Abstract
The Tat protein and the transactivation responsive (TAR) RNA form an essential complex in the HIV lifecycle, and mutations in the basic region of the Tat protein alter this RNA-protein molecular recognition. Here, EPR spectroscopy was used to identify amino acids, flanking an essential arginine of the Tat protein, which contribute to specific and rigid TAR-Tat complex formation by monitoring changes in the mobility of nitroxide spin-labeled TAR RNA nucleotides upon binding. Arginine to lysine N-terminal mutations did not affect TAR RNA interfacial dynamics. In contrast, C-terminal point mutations, R56 in particular, affected the mobility of nucleotides U23 and U38, which are involved in a base-triple interaction in the complex. This report highlights the role of dynamics in specific molecular complex formation and demonstrates the ability of EPR spectroscopy to study interfacial dynamics of macromolecular complexes.
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Affiliation(s)
- Thomas E Edwards
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
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23
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Enam S, Sweet TM, Amini S, Khalili K, Del Valle L. Evidence for Involvement of Transforming Growth Factor β1 Signaling Pathway in Activation of JC Virus in Human Immunodeficiency Virus 1–Associated Progressive Multifocal Leukoencephalopathy. Arch Pathol Lab Med 2004; 128:282-91. [PMID: 14987161 DOI: 10.5858/2004-128-282-efiotg] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
Context.—Progressive multifocal leukoencephalopathy is a fatal demyelinating disease of the central nervous system frequently seen in patients with impaired immune systems, particularly acquired immunodeficiency syndrome. JC virus (JCV), a human neurotropic polyomavirus, is the etiologic infectious agent of this disease.
Objective.—The significantly higher incidence of progressive multifocal leukoencephalopathy in patients with acquired immunodeficiency syndrome than in patients with other immunosuppressive conditions suggests that molecular interactions between human immunodeficiency virus 1 and JCV, via the Tat protein, are responsible for the activation of the JCV enhancer/promoter and the development of progressive multifocal leukoencephalopathy. An indirect mechanism through activation of cytokines, such as transforming growth factor β1 and Smads 3 and 4, may also be responsible for the enhancement of JCV gene expression.
Design.—Immunohistochemical analysis in progressive multifocal leukoencephalopathy samples and chloramphenicol acetyl transferase assays on cell cultures were performed to corroborate this hypothesis.
Results.—The JCV capsid protein VP-1 was found in the nuclei of oligodendrocytes and in the nuclei and cytoplasm of bizarre astrocytes. Human immunodeficiency virus proteins, including p24 and Tat, were detected in the cytoplasm of astrocytes. Tat, but not p24, was detected in oligodendrocytes, suggesting that extracellular Tat accumulates in the nuclei of oligodendrocytes, where JCV gene transcription takes place. High levels of transforming growth factor β1 and Smads 3 and 4 were detected in JCV-infected oligodendrocytes. Results from in vitro studies confirm activation of the JCV early and late promoters by Smads 3 and 4.
Conclusions.—These observations support our model, suggesting that the induction of transforming growth factor β1 by human immunodeficiency virus 1 Tat can stimulate its downstream factors, including Smads 3 and 4, which in turn augment transcription of the JCV promoter in glial cells.
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Affiliation(s)
- Sahnila Enam
- Center for Neurovirology and Cancer Biology, College of Science and Technology, Temple University, Philadelphia, Pa, USA
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24
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Blount KF, Tor Y. Using pyrene-labeled HIV-1 TAR to measure RNA-small molecule binding. Nucleic Acids Res 2003; 31:5490-500. [PMID: 14500811 PMCID: PMC206455 DOI: 10.1093/nar/gkg755] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2003] [Revised: 08/05/2003] [Accepted: 08/05/2003] [Indexed: 11/14/2022] Open
Abstract
To quantitatively understand the binding affinity and target selectivity of small-molecule RNA interactions, it is useful to have a rapid, highly reproducible binding assay that can be readily generalized to different RNA targets. To that end, an assay has been developed and validated for measuring the binding of low-molecular weight ligands to RNA by monitoring the fluorescence of a covalently incorporated fluorophore. As a test system, the fluorescence of a pyrene-derivatized HIV-1 TAR (transactivating response element) RNA was measured upon titration with aminoglycoside antibiotics. The binding isotherms thus obtained fit well with a model for a 1:1 interaction and yield an accurate measure of the equilibrium dissociation constant. Among a series of natural aminoglycosides, the binding affinity correlates with the number of amines, supporting an electrostatic compensation model for binding. Furthermore, the ionic strength dependence confirms that much of the binding energy is electrostatic. Finally, by measuring the binding affinity in the presence of nucleic acid competitors, we confirm that although aminoglycosides show high RNA to DNA selectivity, their selectivity among different RNA targets is sub- optimal. We conclude that this newly developed assay can be generalized to measure the binding affinities and selectivities of a variety of small molecules to a specific RNA target.
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Affiliation(s)
- Kenneth F Blount
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
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25
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Safak M, Khalili K. An overview: Human polyomavirus JC virus and its associated disorders. J Neurovirol 2003; 9 Suppl 1:3-9. [PMID: 12709864 DOI: 10.1080/13550280390195360] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2002] [Accepted: 10/24/2002] [Indexed: 10/20/2022]
Abstract
JC virus (JCV) is a polyomavirus infecting greater than 80% of the human population early in life. Replication of this virus in oligodendrocytes and astrocytes results in the fatal demyelinating disease progressive multifocal leukoencephalopathy (PML) in immunocompromised individuals, most notably acquired immunodeficiency syndrome (AIDS) patients. Moreover, recent studies have pointed to the association of JCV with a variety of brain tumors, including medulloblastoma. The JCV genome encodes for viral early protein, including large and small T antigens and the newly discovered isoform T', at the early phase of infection and the structural proteins VP1, VP2, and VP3 at the late stage of the lytic cycle. In addition, the late gene is responsible for the production of a small nonstructural protein, agnoprotein, whose function is not fully understood. Here, we have summarized some aspects of the JCV genome structure and function, and its associated diseases, including PML and brain tumors.
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Affiliation(s)
- Mahmut Safak
- Center for Neurovirology and Cancer Biology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, USA
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26
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Matsugami A, Kobayashi SI, Ouhashi K, Uesugi S, Yamamoto R, Taira K, Nishikawa S, Kumar PKR, Katahira M. Structural basis of the highly efficient trapping of the HIV Tat protein by an RNA aptamer. Structure 2003; 11:533-45. [PMID: 12737819 DOI: 10.1016/s0969-2126(03)00069-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
An RNA aptamer containing two binding sites exhibits extremely high affinity to the HIV Tat protein. We have determined the structure of the aptamer complexed with two argininamide molecules. Two adjacent U:A:U base triples were formed, which widens the major groove to make space for the two argininamide molecules. The argininamide molecules bind to the G bases through hydrogen bonds. The binding is stabilized through stacking interactions. The structure of the aptamer complexed with a Tat-derived arginine-rich peptide was also characterized. It was suggested that the aptamer structure is similar for both complexes and that the aptamer interacts with two different arginine residues of the peptide simultaneously at the two binding sites, which could explain the high affinity to Tat.
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Affiliation(s)
- Akimasa Matsugami
- Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79-7 Tokiwadai, Hodogaya-ku, 240-8501, Yokohama, Japan
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27
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Abstract
Metal ion-induced changes in HIV-1 TAR RNA internal dynamics were determined by the changes in EPR spectral width for TAR RNAs containing spin-labeled nucleotides (U23, U25, U38, and U40). This gave a dynamic signature for each of 10 metal ions studied, which fell into one of three distinct groups. While Li(+) and K(+) had little effect on TAR RNA internal dynamics, Na(+) unexpectedly had a dynamic signature that was similar to Ca(2+) and Sr(2+), with a decrease in mobility at U23 and U38, little or no change at U25, and an increase in mobility at U40. Mg(2+), Co(2+), Ni(2+), Zn(2+), and Ba(2+) had similar effects on U23, U38, and U40, but the mobility of U25 was markedly increased. Our results show that RNA dynamics change upon metal binding to the TAR RNA bulge, indicating that RNA structure adapts to accommodate metal ions of different size and coordination properties.
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Affiliation(s)
- Thomas E Edwards
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA 98195-1700, USA
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28
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Sweet TM, Del Valle L, Khalili K. Molecular biology and immunoregulation of human neurotropic JC virus in CNS. J Cell Physiol 2002; 191:249-56. [PMID: 12012320 DOI: 10.1002/jcp.10096] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The human polyomavirus, JC virus (JCV), provides an excellent model system to investigate the reciprocal interaction of the immune and nervous systems. Infection with JCV occurs during childhood and the virus remains in the latent state with no apparent clinical symptoms. However, under immunosuppressed conditions, the virus enters the lytic cycle and upon cytolytic destruction of glial cells, causes the fatal demyelinating disease of the central nervous system (CNS), named progressive multifocal leukoencephalopathy (PML). In this short review, we discuss the molecular pathogenesis of PML by highlighting the role of the immune system in modulating JCV gene activation and replication, and the latency/reactivation of this virus upon immunosuppression. Further, due to the higher incidence of PML among AIDS patients, we further elaborate on the cross-talk between JCV and HIV-1 by direct and indirect pathways that lead to enhanced expression of the JCV genome.
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Affiliation(s)
- Thersa M Sweet
- Center for Neurovirology and Cancer Biology, Temple University, Philadelphia, Pennsylvania 19122, USA
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29
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Edwards TE, Okonogi TM, Sigurdsson ST. Investigation of RNA-protein and RNA-metal ion interactions by electron paramagnetic resonance spectroscopy. The HIV TAR-Tat motif. CHEMISTRY & BIOLOGY 2002; 9:699-706. [PMID: 12079781 DOI: 10.1016/s1074-5521(02)00150-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy was used to investigate changes in dynamics of spin-labeled nucleotides in the TAR RNA (U23, U25, U38, and U40) upon binding to cations, argininamide, and two peptides derived from the Tat protein. Nearly identical changes in dynamics were obtained for either calcium or sodium ions, indicating the absence of a calcium-specific structural change for the TAR RNA in solution that had previously been suggested by crystallographic data. Similar dynamic signatures were obtained for two Tat-derived peptides that have the same important binding determinant (R52) and similar binding affinities to the TAR RNA. However, U23 and U38 were substantially less mobile for the wild-type peptide (YGRKKRRQRRR) than for the mutant (YKKKKRKKKKA), demonstrating that, flanking R52, amino acids in the wild-type sequence make specific contacts to the RNA.
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Affiliation(s)
- Thomas E Edwards
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
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30
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Bennasser Y, Bahraoui E. HIV-1 Tat protein induces interleukin-10 in human peripheral blood monocytes: involvement of protein kinase C-betaII and -delta. FASEB J 2002; 16:546-54. [PMID: 11919157 DOI: 10.1096/fj.01-0775com] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In HIV-infected patients, production of interleukin-10 (IL-10), a highly immunosuppressive cytokine, is associated with the disease progression toward AIDS. We have previously shown that HIV-1 Tat induces IL-10 production by human monocytes via a protein kinase C (PKC) -dependent pathway. Here we show that PKC activation by Tat is essential for IL-10 induction. Among the eight PKC isoforms present in human monocytes, we investigated which isoform(s) plays this crucial role in Tat-mediated IL-10 production and show that 1) Tat can activate PKC-alpha, PKC-betaII, PKC-delta, and PKC-epsilon, 2) of these four potential candidates, only PKC-betaII, PKC-delta, and PKC-epsilon are activated by the active domain Tat 1-45, which is responsible for IL-10 production and depleted by long-term exposure to PMA, which abolishes Tat-mediated IL-10 production, 3) whereas selective inhibition of PKC-alpha and PKC-epsilon by specific antisense oligonucleotides has no effect on Tat-mediated IL-10 induction, inhibition of either PKC-betaII or PKC-delta partially inhibits IL-10 production; and 4) the simultaneous inhibition of PKC-betaII and PKC-delta totally inhibits Tat-mediated IL-10. Altogether, these results suggest that the induction of IL-10 by Tat is strictly dependent on the PKC-delta and -betaII isoforms.
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Affiliation(s)
- Yamina Bennasser
- Laboratoire d'Immuno-Virologie, EA 3038, Université Paul Sabatier, 31062 Toulouse, France
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31
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Piccinini M, Rinaudo MT, Chiapello N, Ricotti E, Baldovino S, Mostert M, Tovo PA. The human 26S proteasome is a target of antiretroviral agents. AIDS 2002; 16:693-700. [PMID: 11964525 DOI: 10.1097/00002030-200203290-00004] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Proteasomes constitute the degradative machinery of the ubiquitin/adenosine triphosphate-dependent proteolytic pathway, which is involved in many cell functions, including immune response and apoptosis, and in HIV maturation and infectivity. OBJECTIVE To examine whether proteasomes are targeted by antiretroviral agents. METHODS Chymotrypsin-like, trypsin-like and peptidyl-glutamyl-peptide hydrolysing activities of purified human 26S and 20S proteasomes, the latter depleted or enriched in 11S regulator, were assayed after incubation with indinavir, lamivudine and zidovudine at 1-80 microM alone and in combination. To assess the drug effects on cellular functions regulated by proteasomes, the accumulation of ubiquitin-tagged proteins, the processing of the nuclear factor kappa B precursor p105, and the degradation of the inhibitor of nuclear factor kappa B, isoform alpha (IkappaBalpha) were evaluated by Western immunoblotting in Jurkat cells after incubation for 6 h with the drugs above. RESULTS Trypsin-like and mostly chymotrypsin-like activities of purified 26S proteasome were inhibited by each drug from 10 to 80 microM, more by double combinations and mostly by the triple combination. The peptidyl-glutamyl-peptide hydrolysing activity of the 26S proteasome and the three peptidase activities of the 20S proteasome, depleted or enriched in 11S regulator, were unaffected. The accumulation of ubiquitin-tagged proteins, reduced IkappaBalpha degradation and p105 processing were appreciable in intact cells with the triple drug combination. CONCLUSION The human 26S proteasome is a target of antiretroviral agents. This suggests that the antiviral action and some clinical and immunological benefits of combined antiretroviral therapy rely not only on its known effects on viral enzymes, but also on host cell components.
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Affiliation(s)
- Marco Piccinini
- Department of Medicine and Experimental Oncology, Section of Biochemistry, University of Turin, Turin, Italy
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32
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Al-Hashimi HM, Gosser Y, Gorin A, Hu W, Majumdar A, Patel DJ. Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings. J Mol Biol 2002; 315:95-102. [PMID: 11779230 DOI: 10.1006/jmbi.2001.5235] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Ground-state dynamics in RNA is a critical precursor for structural adaptation observed ubiquitously in protein-RNA recognition. A tertiary conformational analysis of the stem-loop structural element in the transactivation response element (TAR) from human immunodeficiency virus type 1 (HIV-I) RNA is presented using recently introduced NMR methods that rely on the measurement of residual dipolar couplings (RDC) in partially oriented systems. Order matrix analysis of RDC data provides evidence for inter-helical motions that are of amplitude 46(+/-4) degrees, of random directional character, and that are executed about an average conformation with an inter-helical angle between 44 degrees and 54 degrees. The generated ensemble of TAR conformations have different organizations of functional groups responsible for interaction with the trans-activator protein Tat, including conformations similar to the previously characterized bound-state conformation. These results demonstrate the utility of RDC-NMR for simultaneously characterizing RNA tertiary dynamics and average conformation, and indicate an avenue for TAR complex formation involving tertiary structure capture.
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Affiliation(s)
- Hashim M Al-Hashimi
- Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.
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33
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Jia H, Lohr M, Jezequel S, Davis D, Shaikh S, Selwood D, Zachary I. Cysteine-rich and basic domain HIV-1 Tat peptides inhibit angiogenesis and induce endothelial cell apoptosis. Biochem Biophys Res Commun 2001; 283:469-79. [PMID: 11327725 DOI: 10.1006/bbrc.2001.4790] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Previous findings suggest that both the Tat polypeptide encoded by HIV-1 and Tat-derived peptides can induce angiogenesis via activation of the KDR receptor for Vascular Endothelial Growth Factor (VEGF). We identified 20 amino acids and 12 amino acid peptides corresponding to the cysteine-rich and basic domains of HIV-1 Tat which inhibited (125)I-VEGF(165) binding to KDR and neuropilin-1 (NP-1) receptors in endothelial cells. Cysteine-rich and basic Tat peptides inhibited VEGF-induced ERK activation and mitogenesis in endothelial cells, and inhibited angiogenesis in vitro at concentrations similar to those which inhibited VEGF receptor binding. These peptides also inhibited proliferation, angiogenesis, and ERK activation induced by basic fibroblast growth factor with similar potency and efficacy. Surprisingly, we found that both cysteine-rich and basic domain Tat peptides strikingly induced apoptosis in endothelial cells, independent of their effects on VEGF and bFGF. Furthermore, we found no evidence for direct biological effects of recombinant Tat on VEGF receptor binding, ERK activation, endothelial cell survival, or mitogenesis. These findings demonstrate novel properties of Tat-derived peptides and indicate that their major effect in endothelial cells is apoptosis independent of specific inhibition of VEGF receptor activation.
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MESH Headings
- Amino Acid Sequence
- Apoptosis/drug effects
- Cells, Cultured
- Cysteine/chemistry
- Endothelial Growth Factors/metabolism
- Endothelium, Vascular/cytology
- Endothelium, Vascular/drug effects
- Endothelium, Vascular/metabolism
- Enzyme Activation/drug effects
- Fibroblast Growth Factor 2/pharmacology
- Gene Products, tat/chemistry
- Gene Products, tat/genetics
- Gene Products, tat/pharmacology
- Humans
- Lymphokines/metabolism
- Mitogen-Activated Protein Kinases/metabolism
- Molecular Sequence Data
- Neovascularization, Physiologic/drug effects
- Peptide Fragments/chemistry
- Peptide Fragments/genetics
- Peptide Fragments/toxicity
- Protein Structure, Tertiary
- Receptor Protein-Tyrosine Kinases/drug effects
- Receptor Protein-Tyrosine Kinases/metabolism
- Receptors, Growth Factor/drug effects
- Receptors, Growth Factor/metabolism
- Receptors, Vascular Endothelial Growth Factor
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/pharmacology
- Vascular Endothelial Growth Factor A
- Vascular Endothelial Growth Factors
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Affiliation(s)
- H Jia
- Department of Medicine, Ark Therapeutics Limited, London, WC1E 6JJ, United Kingdom
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34
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Van Lint C. Role of chromatin in HIV-1 transcriptional regulation. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2001; 48:121-60. [PMID: 10987090 DOI: 10.1016/s1054-3589(00)48005-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- C Van Lint
- Département de Biologie Moléculaire, Université Libre de Bruxelles, Gosselies, Belgium
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35
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Arese M, Ferrandi C, Primo L, Camussi G, Bussolino F. HIV-1 Tat protein stimulates in vivo vascular permeability and lymphomononuclear cell recruitment. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2001; 166:1380-8. [PMID: 11145723 DOI: 10.4049/jimmunol.166.2.1380] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
HIV-1 Tat protein released by infected cells is a chemotactic molecule for leukocytes and induces a proinflammatory program in endothelial cells (EC) by activating vascular endothelial growth factor (VEGF) receptors expressed on both cell types. Its potential role in causing vascular permeability and leukocyte recruitment was studied in vivo following its s.c. injection in mice. Tat caused a dose-dependent early (15 min) and late (6 h) wave of permeability that were inhibited by a neutralizing Ab anti-VEGF receptor type 2. Tissue infiltration of lymphomononuclear cells, mainly monocytes (76%), was evident at 6 h and persisted up to 24 h. WEB2170, a platelet activating factor (PAF) receptor antagonist, reduced the early leakage by 70-80%, but only slightly inhibited the late wave and cell recruitment. In vitro, Tat induced a dose-dependent flux of albumin through the EC monolayer that was inhibited by Ab anti-vascular VEGF receptor type 2 and WEB2170, and PAF synthesis in EC that was blocked by the Ab anti-VEGF receptor type 2. Lastly, an anti-monocyte chemotactic peptide-1 (MCP-1) Ab significantly reduced the lymphomononuclear infiltration elicited by Tat. In vitro, Tat induced a dose-dependent production of MCP-1 by EC after a 24-h stimulation. These results highlighted the role of PAF and MCP-1 as secondary mediators in the onset of lymphomononuclear cell recruitment in tissues triggered by Tat.
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Affiliation(s)
- M Arese
- Institute for Cancer Research and Treatment and Department of Genetics, Biology and Biochemistry, School of Medicine, University of Torino, Candiolo. Italy
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36
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Peasley K. A nucleoside analogue of 2, 4-difluoropyridine has potential as an antiretroviral agent with multiple and unique mechanisms of action, and may be effective against the HIV organism. Med Hypotheses 2000; 55:408-14. [PMID: 11058420 DOI: 10.1054/mehy.2000.1077] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The high rate of mutation which is inherent in reverse transcription of the HIV genome is a result of the lack of proof-reading function of the reverse transcriptase enzyme. This has allowed the HIV virus to develop resistance to multiple antiviral agents. It may be possible to use this viral property to advantage by treatment with an antiviral nucleoside analogue which is a close structural isostere of uridine and deoxyuridine. The drug is unable to form hydrogen bonds with adenine and will be excluded from host cell DNA by its 3' to 5' proof-reading exonuclease activity. However, reverse transcriptase, which has no such mechanism, will allow incorporation of the drug into proviral DNA. The drug will have an inhibitory effect on RNase H function. It will also be expected to cause delay in elongation at those sites in the template strand that contain two or more adjacent adenine bases, because two drug molecules will, for practical purposes, never be inserted in the same strand next to each other. The length of the delay in strand elongation will therefore be a function of the availability of the natural NTP or dNTP. Both the rate and fidelity of protein synthesis will be affected by the drug. There will be decreased stability of the proviral double stranded DNA and if the proviral DNA is able to integrate into the host cell chromosome, double stranded breaks may be produced by the host cells' DNA repair mechanisms. Finally there will be a specific 'strand trade' mutation that the drug will induce specifically into viral but not into cellular genetic material.
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37
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Mischiati C, Feriotto G, Borgatti M, Giacomini P, Gambari R. Characterization of a major histocompatibility complex class II X-box-binding protein enhancing tat-induced transcription directed by the human immunodeficiency virus type 1 long terminal repeat. J Virol 2000; 74:8989-9001. [PMID: 10982343 PMCID: PMC102095 DOI: 10.1128/jvi.74.19.8989-9001.2000] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The X-box element present within the promoter region of genes belonging to the major histocompatibility complex (MHC) plays a pivotal role in the expression of class II molecules, since it contains the binding sites for several well-characterized transcription factors. We have analyzed a randomly selected compilation of viral genomes for the presence of elements homologous to the X box of the HLA-DRA gene. We found that human immunodeficiency virus type 1 (HIV-1) shows the highest frequency of X-like box elements per 1,000 bases of genome. Within the HIV-1 genome, we found an X-like motif in the TAR region of the HIV-1 long terminal repeat (LTR), a regulative region playing a pivotal role in Tat-induced HIV-1 transcription. The use of a decoy approach for nuclear proteins binding to this element, namely, XMAS (X-like motif activator sequence), performed by transfection of multiple copies of this sequence into cells carrying an integrated LTR-chloramphenicol acetyltransferase construct, suggests that this element binds to nuclear proteins that enhance Tat-induced transcription. In this report we have characterized two proteins, one binding to the XMAS motif and the other to the flanking regions of XMAS. Mobility shift assays performed on crude nuclear extracts or enriched fractions suggest that similar proteins bind to XMAS from HIV-1 and the X box of the HLA-DRA gene. Furthermore, a UV cross-linking assay suggests that one protein of 47 kDa, termed FAX (factor associated with XMAS)-1, binds to the XMAS of HIV-1. The other protein of 56 kDa was termed FAX-2. In a decoy ex vivo experiment, it was found that sequences recognizing both proteins are required to inhibit Tat-induced HIV-1 LTR-driven transcription. Taken together, the data reported in this paper suggest that XMAS and nearby sequences modulate Tat-induced HIV-1 transcription by binding to the X-box-binding proteins FAX-1 and FAX-2. The sequence homology between XMAS and X box is reflected in binding of a common protein, FAX-1, and similar functional roles in gene expression. To our knowledge, this is the first report showing that transcription factors binding to the X box of the MHC class II genes enhance the transcription of HIV-1.
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Affiliation(s)
- C Mischiati
- Department of Biochemistry and Molecular Biology, University of Ferrara, Ferrara, Italy.
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38
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Synthesis of Alanine and Proline Amino Acids with Amino or Guanidinium Substitution on the Side Chain. Tetrahedron 2000. [DOI: 10.1016/s0040-4020(00)00123-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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39
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Taube R, Fujinaga K, Wimmer J, Barboric M, Peterlin BM. Tat transactivation: a model for the regulation of eukaryotic transcriptional elongation. Virology 1999; 264:245-53. [PMID: 10562489 DOI: 10.1006/viro.1999.9944] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- R Taube
- Department of Medicine, University of California, San Francisco, San Francisco, California, 94143-0703, USA
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40
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Germinario RJ, Colby-Germinario SP, Acel A, Chandok R, Davison K, Mak J, Kleiman L, Faust E, Wainberg MA. Effect of insulin-like growth factor I on HIV type 1 long terminal repeat-driven chloramphenicol acetyltransferase expression. AIDS Res Hum Retroviruses 1999; 15:829-36. [PMID: 10381171 DOI: 10.1089/088922299310737] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In this study, we have investigated the ability of insulin-like growth factor I (IGF-I) to inhibit HIV long terminal repeat (LTR)-driven gene expression. Using COS 7 cells cotransfected with tat and an HIV LTR linked to a chloramphenicol acetyltransferase (CAT) reporter, we observed that physiological levels of IGF-I (10(-9) M) significantly inhibited CAT expression in a concentration- and time-dependent manner. IGF-I did not inhibit CAT expression in COS 7 cells transfected with pSVCAT, and did not affect CAT expression in the absence of cotransfection with tat. Transfection of HIV-1 proviral DNA into COS 7 cells +/- IGF-I resulted in a significant decrease (p < 0.05) in infectious virion production. Both IGF-I and Ro24-7429 inhibited LTR-driven CAT expression, while TNF-alpha-enhanced CAT expression was not affected by IGF-I. On the other hand, a plasmid encoding parathyroid hormone-related peptide exhibited dramatic additivity of inhibition of CAT expression in COS 7 cells. Finally, we show that in Jurkat or U937 cells cotransfected with HIVLTRCAT/tat, IGF-I significantly inhibited CAT expression. Further, interleukin 4 showed in U937 cells inhibition of CAT expression that was not additive to IGF-I induced inhibition. Our data demonstrate that IGF-I can specifically inhibit HIVLTRCAT expression. This inhibition may occur at the level of the tat/TAR interaction. Finally, this IGF-I effect is seen in target cell lines and similar paths of inhibition may be involved in the various cell types employed.
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Affiliation(s)
- R J Germinario
- Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Montreal, Quebec, Canada
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41
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Litovchick A, Evdokimov AG, Lapidot A. Arginine-aminoglycoside conjugates that bind to HIV transactivation responsive element RNA in vitro. FEBS Lett 1999; 445:73-9. [PMID: 10069377 DOI: 10.1016/s0014-5793(99)00092-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
HIV gene expression is crucially dependent on binding of the viral Tat protein to the transactivation RNA response element. A number of synthetic Tat-transactivation responsive element interaction inhibitors of peptide/peptoid nature were described as potential antiviral drug prototypes. We present a new class of peptidomimetic inhibitors, conjugates of L-arginine with aminoglycosides. Using a gel-shift assay and affinity chromatography on an L-arginine column we found that these compounds bind specifically to the transactivation responsive element RNA in vitro with Kd values in the range of 20-400 nM, which is comparable to the Kd of native Tat bound to the transactivation responsive element (10-12 nM). Confocal microscopy studies demonstrated that fluorescein-labelled conjugate penetrates into live cells. High affinity to the transactivation responsive element, low toxicity, and relative simplicity of synthesis make these compounds attractive candidates for antiviral drug design.
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Affiliation(s)
- A Litovchick
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot, Israel
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42
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Farese-Di Giorgio A, Pairot S, Patino N, Condom R, Di Giorgio C, Aumelas A, Aubertin AM, Guedj R. Synthesis of a new class of HIV-1 inhibitors. NUCLEOSIDES & NUCLEOTIDES 1999; 18:263-75. [PMID: 10067276 DOI: 10.1080/15257779908043073] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
A new family of molecules potentially inhibitors of the HIV-1 Tat-TAR complex was prepared. These compounds are constituted by dinucleotide analogs (PNA dimer) bound, through a linker, to an arginine residue. In this series, several molecules inhibit viral development in cell culture with a micromolar IC50 and without cellular toxicity until 200 microM concentration.
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Affiliation(s)
- A Farese-Di Giorgio
- Laboratoire de Chimie Bio-Organique, CNRS ESA 6001, Université de Nice Sophia-Antipolis, France
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43
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Powell JD, Ragheb JA, Kitagawa-Sakakida S, Schwartz RH. Molecular regulation of interleukin-2 expression by CD28 co-stimulation and anergy. Immunol Rev 1998; 165:287-300. [PMID: 9850868 DOI: 10.1111/j.1600-065x.1998.tb01246.x] [Citation(s) in RCA: 156] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The consequences of T-cell receptor engagement (signal 1) are profoundly affected by the presence or absence of co-stimulation (signal 2). T-cell receptor (TCR) stimulation in the absence of CD28-mediated co-stimulation not only results in little interleukin (IL)-2 production, but induces a long lasting hyporesponsive state known as T-cell clonal anergy. The addition of CD28 ligation to signal 1, on the other hand, results in the production of copious amounts of IL-2. Our laboratory has utilized CD4+ Th 1 clones in an effort to understand the molecular events resulting in enhanced IL-2 production by co-stimulation and the inhibition of IL-2 production in anergy. Our current studies have focused on defining the post-transcriptional effects of CD28-enhanced IL-2 production. The data suggest that a major component of CD28's ability to regulate IL-2 production occurs at the level of message stability and involves the 3'-untranslated region of the message. In terms of anergy, our recent studies support the notion that it is not the result of TCR engagement in the absence of co-stimulation, but rather signal 1 in the absence of IL-2 receptor signaling and proliferation. Furthermore, T-cell anergy appears to be an active negative state in which IL-2 production is inhibited both at the level of signal transduction and by cis-dominant repression at the level of the IL-2 promoter.
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Affiliation(s)
- J D Powell
- Laboratory of Cellular and Molecular Immunology, National Institutes of Health, Bethesda, MD 20892-0420, USA
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Shoji S, Furuishi K, Ogata A, Yamataka K, Tachibana K, Mukai R, Uda A, Harano K, Matsushita S, Misumi S. An allosteric drug, o,o'-bismyristoyl thiamine disulfide, suppresses HIV-1 replication through prevention of nuclear translocation of both HIV-1 Tat and NF-kappa B. Biochem Biophys Res Commun 1998; 249:745-53. [PMID: 9731208 DOI: 10.1006/bbrc.1998.9221] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The efficacy of o,o'-bismyristoyl thiamine disulfide (BMT) was examined in detail against HIV-1 laboratory isolates (HTLV-IIIB, JRFL, and MN), primary isolates (KMT and KMO), and simian immunodeficiency virus (SIVmac251) in vitro. BMT inhibited the replication of HIV-1 in both laboratory and primary isolates in vitro. In addition, BMT exhibited antiviral activity against SIVmac251. Minimizing energy studies of BMT structure reveal that a trans-disulfide of thiamine (holo drug) disulfide (TDS, protodrug) is allosterically transited to the reactive twisted disulfide of BMT (allo drug) by o,o'-bismyristoyl esterification of TDS. BMT inhibits nuclear translocation of both HIV-1 transactivator (TAT) and the cellular transcriptional nuclear factor-KB (NF-kappa B), resulting in the suppression of HIV-1 replication.
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Affiliation(s)
- S Shoji
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Kumamoto University, Japan.
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45
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Brodsky AS, Erlacher HA, Williamson JR. NMR evidence for a base triple in the HIV-2 TAR C-G.C+ mutant-argininamide complex. Nucleic Acids Res 1998; 26:1991-5. [PMID: 9518494 PMCID: PMC147484 DOI: 10.1093/nar/26.8.1991] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Formation of a specific complex between the HIV Tat protein and the small RNA element TAR is critical for activation of viral transcription. A model complex for this interaction composed of HIV-2 TAR and the amide derivative of arginine has been developed to study how Tat and TAR interact specifically. We have previously determined a high resolution NMR structure of the HIV-2 TAR-argininamide complex. The argininamide guanidium group hydrogen bonds to the major groove face of G26 and is stacked between U23 and A22, forming an arginine sandwich. This structure also provided evidence for formation of a U38-A27.U38 base triple, as U23 is positioned in the major groove within hydrogen bonding distance to A27. However, the expected U23 imino proton was not observed, preventing unambiguous identification of the base triple. Previous work on an isomorphic C38-G27.C23+ base triple mutant of the three base bulge HIV-1 TAR-argininamide complex demonstrated that the base triple is required for specific argininamide binding. Here we investigate the same C38-G27.C23+ base triple mutant in the context of two base bulge HIV-2 TAR. The improved NMR spectral properties of HIV-2 TAR allowed observation of the C23 amino and imino protons for the first time, providing direct evidence that a hydrogen bonding interaction is occurring. The NOEs observed correspond to those observed in the high resolution structure of the HIV-2 TAR-argininamide complex, confirming that a base triple is an important feature of the TAR-argininamide interaction.
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Affiliation(s)
- A S Brodsky
- MIT Department of Chemistry, Building 56-546, Cambridge, MA 02139, USA
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Benelli R, Mortarini R, Anichini A, Giunciuglio D, Noonan DM, Montalti S, Tacchetti C, Albini A. Monocyte-derived dendritic cells and monocytes migrate to HIV-Tat RGD and basic peptides. AIDS 1998; 12:261-8. [PMID: 9517988 DOI: 10.1097/00002030-199803000-00003] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
OBJECTIVE AND DESIGN Extracellular Tat released from HIV-1-infected cells is a mitogenic and motogenic factor for endothelial and Kaposi's sarcoma (KS)-derived cells and is angiogenic in vivo. Here we show for the first time that Tat induces migration of human dendritic cells in a concentration-dependent manner and that the Arg-Gly-Asp (RGD) and basic Tat peptides contribute to dendritic and monocyte cell migration. In vivo, Tat stimulates invasion of macrophages into a matrigel sponge. METHODS Monocyte and dendritic cell chemotaxis was assessed using the Boyden chamber assay. RESULTS Tat induced migration of monocyte-derived dendritic cells at the same levels as the N-formyl-Met-Leu-Phe peptide, and of monocytes at levels comparable to RANTES. Peptide mapping of the chemotactic activity of Tat showed that the RGD domain, which has been shown to support integrin-mediated cell migration, and the basic domain which binds and activates the tyrosine kinase receptor KDR on endothelial cells, both had activity. Antibody-blocking experiments indicate that responses to the RGD domain was inhibited by beta1 and alpha vbeta3 integrin blocking antibodies. Combination of the Tat RGD and basic peptides did not show additive effects; however, Tat co-operated with macrophage-chemotactic protein or RANTES in inducing monocyte migration. CONCLUSIONS Our results show that Tat can act as a chemoattractant for dendritic cells, and that both the RGD and basic domains are involved in this response. These same domains attract monocytes. The alpha vbeta3 and beta1 integrins are equally involved in Tat-induced monocyte migration, while the alpha vbeta3 integrin largely mediates the dendritic cell response to Tat.
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Affiliation(s)
- R Benelli
- Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
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47
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Sannes-Lowery KA, Hu P, Mack DP, Mei HY, Loo JA. HIV-1 Tat peptide binding to TAR RNA by electrospray ionization mass spectrometry. Anal Chem 1997; 69:5130-5. [PMID: 9414617 DOI: 10.1021/ac970745w] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Electrospray ionization mass spectrometry (ESI-MS) has been used to study the noncovalent complexes formed from the interaction between HIV-1 Tat peptide and Tat protein with TAR RNA. Both positive ion and negative ion ESI mass spectra showed a maximum stoichiometry of 3:1 between Tat peptide and TAR RNA. However, the higher order complexes only occurred at high relative concentrations of Tat peptide. The 1:1 Tat peptide-TAR RNA complex is believed to involve only specific interactions, whereas the higher order complexes involve nonspecific interactions. Relative binding affinities between Tat peptide and TAR RNA and its various mutants (TAR missing the three-nucleotide bulge, TAR with a poly(ethylene glycol) linker in the bulge region, and TAR with a poly(ethylene glycol) linker in the loop region) can be differentiated by competitive binding experiments and ESI-MS measurements. The gas phase mass spectrometry experiments are consistent with solution phase studies, as they show that mutations in the bulge region reduce TAR RNA affinity to Tat peptide.
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Affiliation(s)
- K A Sannes-Lowery
- Chemistry Department, Parke-Davis Pharmaceutical Research, Division of Warner-Lambert Company, Ann Arbor, Michigan 48105, USA
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48
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Greenberg ME, Mathews MB. Effects of heterologous downstream sequences on the activity of the HIV-1 promoter and its response to Tat. Nucleic Acids Res 1997; 25:5017-24. [PMID: 9396810 PMCID: PMC147141 DOI: 10.1093/nar/25.24.5017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
In HIV-1 infection, Tat acts at least in part to control transcriptional elongation by overcoming premature transcriptional termination. In some other genes this process is governed by DNA elements called attenuators in concert with cellular transcription factors. To understand the action of Tat more fully and explore its role as an anti-attenuator, we examined the ability of several natural and synthetic attenuation sequences to modulate transcription initiated at the HIV LTR. Fragments containing these signals were inserted downstream of the TAR element in an HIV-CAT chimera and their effects on transcription were assessed both in vitro and in vivo. Runoff transcription assays in HeLa cell extracts demonstrated that the attenuators give rise to premature termination of transcripts initiated from the heterologous HIV-LTR promoter in vitro. When transiently expressed following transfection into Cos cells, however, premature transcript termination at the attenuation site was not observed. Nevertheless, many of the inserted sequences exerted marked effects on CAT gene expression and on transactivation by Tat at both the RNA and protein levels. The nature and magnitude of the effects depended upon the identity of the attenuator and its orientation but only one of 16 sequences tested met the criteria for a Tat-suppressible attenuator in vivo. One other sequence, in contrast, severely reduced Tat-activated transcription without inhibiting basal transcription These results indicate that sequences downstream of the HIV LTR can influence its function as a promoter and its response to Tat transactivation, but lend little support to their role as attenuators in vivo.
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Affiliation(s)
- M E Greenberg
- Cold Spring Harbor Laboratory, PO Box 100, Cold Spring Harbor, NY 11724, USA
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Liang C, Li X, Quan Y, Laughrea M, Kleiman L, Hiscott J, Wainberg MA. Sequence elements downstream of the human immunodeficiency virus type 1 long terminal repeat are required for efficient viral gene transcription. J Mol Biol 1997; 272:167-77. [PMID: 9299345 DOI: 10.1006/jmbi.1997.1239] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We investigated the role of a 54-nucleotide region (+200 to +253) located downstream of the HIV-1 long terminal repeat (LTR) on virus gene expression and found, using RT-PCR and p24 CA analysis, that deletion of this region inhibited synthesis of both viral RNA and protein. CAT assays showed that these results were attributable to decreased transcription efficiency of the HIV-1 LTR and not to the stability of the RNA transcripts produced. Further deletional analysis and transfection studies showed that the most important sequences with regard to proviral DNA expression were located between nucleotide positions +218 and +237. Furthermore, substitutional mutational analysis showed that a CTCTCTC sequence at positions +227 to +233, homologous to the pyrimidine-rich initiator (Inr) region found in several promoters, was required for efficient production of both viral RNA and protein. Deletion of the sequence +200 to +217, homologous to the interferon-stimulated response element (ISRE), resulted in impaired LTR promoter activity and decreased synthesis of viral RNA and protein. However, when the latter region was replaced by homologous ISRE sequences from an interferon-stimulated gene (ISG-54), an even more severe effect on HIV gene expression and replication was observed, suggesting that ISRE-like sequences in HIV act differently from homologous sequences in interferon-responsive cellular genes.
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Affiliation(s)
- C Liang
- McGill University Aids Centre, Jewish General Hospital, 3755 Cote Ste-Catherine Road, Montreal, Quebec, Canada
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Schrader T. Strong Binding of Alkylguanidinium Ions by Molecular Tweezers: An Artificial Selective Arginine Receptor Molecule with a Biomimetic Recognition Pattern. Chemistry 1997. [DOI: 10.1002/chem.19970030923] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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