101
|
Jackson PE, Tebit DM, Rekosh D, Hammarskjold ML. Rev-RRE Functional Activity Differs Substantially Among Primary HIV-1 Isolates. AIDS Res Hum Retroviruses 2016; 32:923-34. [PMID: 27147495 DOI: 10.1089/aid.2016.0047] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The HIV-1 replication cycle requires the nucleocytoplasmic export of intron-containing viral RNAs, a process that is ordinarily restricted. HIV overcomes this by means of the viral Rev protein, which binds to an RNA secondary structure called the Rev response element (RRE) present in all unspliced or incompletely spliced viral RNA transcripts. The resulting mRNP complex is exported through interaction with cellular factors. The Rev-RRE binding interaction is increasingly understood to display remarkable structural plasticity, but little is known about how Rev-RRE sequence differences affect functional activity. To study this issue, we utilized a lentiviral vector assay in which vector titer is dependent on the activity of selected Rev-RRE pairs. We found that Rev-RRE functional activity varies significantly (up to 24-fold) between naturally occurring viral isolates. The activity differences of the Rev-RRE cognate pairs track closely with Rev, but not with RRE activity. This variation in Rev activity is not correlated with differences in Rev steady state protein levels. These data suggest that Rev sequence differences drive substantial variation in Rev-RRE functional activity between patients. Such variation may play a role in viral adaptation to different immune milieus within and between patients and may be significant in the establishment of latency. The identification of differences in Rev-RRE functional activity in naturally occurring isolates may also permit more efficient production of lentiviral vectors.
Collapse
Affiliation(s)
- Patrick E. Jackson
- Department of Microbiology, Immunology, and Cancer Biology, Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia
| | - Denis M. Tebit
- Department of Microbiology, Immunology, and Cancer Biology, Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia
| | - David Rekosh
- Department of Microbiology, Immunology, and Cancer Biology, Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia
| | - Marie-Louise Hammarskjold
- Department of Microbiology, Immunology, and Cancer Biology, Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia
| |
Collapse
|
102
|
Jayaraman B, Smith AM, Fernandes JD, Frankel AD. Oligomeric viral proteins: small in size, large in presence. Crit Rev Biochem Mol Biol 2016; 51:379-394. [PMID: 27685368 DOI: 10.1080/10409238.2016.1215406] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Viruses are obligate parasites that rely heavily on host cellular processes for replication. The small number of proteins typically encoded by a virus is faced with selection pressures that lead to the evolution of distinctive structural properties, allowing each protein to maintain its function under constraints such as small genome size, high mutation rate, and rapidly changing fitness conditions. One common strategy for this evolution is to utilize small building blocks to generate protein oligomers that assemble in multiple ways, thereby diversifying protein function and regulation. In this review, we discuss specific cases that illustrate how oligomerization is used to generate a single defined functional state, to modulate activity via different oligomeric states, or to generate multiple functional forms via different oligomeric states.
Collapse
Affiliation(s)
- Bhargavi Jayaraman
- a Department of Biochemistry and Biophysics , University of California , San Francisco , CA , USA
| | - Amber M Smith
- a Department of Biochemistry and Biophysics , University of California , San Francisco , CA , USA
| | - Jason D Fernandes
- b UC Santa Cruz Genomics Institute , Santa Cruz , CA , USA.,c Howard Hughes Medical Institute, University of California , Santa Cruz , CA , USA
| | - Alan D Frankel
- a Department of Biochemistry and Biophysics , University of California , San Francisco , CA , USA
| |
Collapse
|
103
|
Wynn JE, Zhang W, Tebit DM, Gray LR, Hammarskjold ML, Rekosh D, Santos WL. Effect of intercalator and Lewis acid-base branched peptide complex formation: boosting affinity towards HIV-1 RRE RNA. MEDCHEMCOMM 2016; 7:1436-1440. [PMID: 27453773 DOI: 10.1039/c6md00171h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
High throughput screening of a 4096 compound library of boronic acid and acridine containing branched peptides revealed compounds that have dissociation constants in the low nanomolar regime for HIV-1 RRE IIB RNA. We demonstrate that branched peptide boronic acids A5, A6, and A7 inhibit the production of p24, an HIV-1 capsid protein, in a dose-dependent manner.
Collapse
Affiliation(s)
- Jessica E Wynn
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24060, USA
| | - Wenyu Zhang
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24060, USA
| | - Denis M Tebit
- Department of Microbiology, Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, VA 22904, USA
| | - Laurie R Gray
- Department of Microbiology, Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, VA 22904, USA
| | - Marie-Louise Hammarskjold
- Department of Microbiology, Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, VA 22904, USA
| | - David Rekosh
- Department of Microbiology, Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, VA 22904, USA
| | - Webster L Santos
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24060, USA
| |
Collapse
|
104
|
DiMattia MA, Watts NR, Cheng N, Huang R, Heymann JB, Grimes JM, Wingfield PT, Stuart DI, Steven AC. The Structure of HIV-1 Rev Filaments Suggests a Bilateral Model for Rev-RRE Assembly. Structure 2016; 24:1068-80. [PMID: 27265851 DOI: 10.1016/j.str.2016.04.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 04/21/2016] [Accepted: 04/25/2016] [Indexed: 11/24/2022]
Abstract
HIV-1 Rev protein mediates the nuclear export of viral RNA genomes. To do so, Rev oligomerizes cooperatively onto an RNA motif, the Rev response element (RRE), forming a complex that engages with the host nuclear export machinery. To better understand Rev oligomerization, we determined four crystal structures of Rev N-terminal domain dimers, which show that they can pivot about their dyad axis, giving crossing angles of 90° to 140°. In parallel, we performed cryoelectron microscopy of helical Rev filaments. Filaments vary from 11 to 15 nm in width, reflecting variations in dimer crossing angle. These structures contain additional density, indicating that C-terminal domains become partially ordered in the context of filaments. This conformational variability may be exploited in the assembly of RRE/Rev complexes. Our data also revealed a third interface between Revs, which offers an explanation for how the arrangement of Rev subunits adapts to the "A"-shaped architecture of the RRE in export-active complexes.
Collapse
Affiliation(s)
- Michael A DiMattia
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Headington OX3 7BN, UK
| | - Norman R Watts
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Naiqian Cheng
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rick Huang
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - J Bernard Heymann
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jonathan M Grimes
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Headington OX3 7BN, UK; Diamond House, Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Paul T Wingfield
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - David I Stuart
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Headington OX3 7BN, UK; Diamond House, Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Alasdair C Steven
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|
105
|
HIV-1 and M-PMV RNA Nuclear Export Elements Program Viral Genomes for Distinct Cytoplasmic Trafficking Behaviors. PLoS Pathog 2016; 12:e1005565. [PMID: 27070420 PMCID: PMC4829213 DOI: 10.1371/journal.ppat.1005565] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Accepted: 03/21/2016] [Indexed: 12/15/2022] Open
Abstract
Retroviruses encode cis-acting RNA nuclear export elements that override nuclear retention of intron-containing viral mRNAs including the full-length, unspliced genomic RNAs (gRNAs) packaged into assembling virions. The HIV-1 Rev-response element (RRE) recruits the cellular nuclear export receptor CRM1 (also known as exportin-1/XPO1) using the viral protein Rev, while simple retroviruses encode constitutive transport elements (CTEs) that directly recruit components of the NXF1(Tap)/NXT1(p15) mRNA nuclear export machinery. How gRNA nuclear export is linked to trafficking machineries in the cytoplasm upstream of virus particle assembly is unknown. Here we used long-term (>24 h), multicolor live cell imaging to directly visualize HIV-1 gRNA nuclear export, translation, cytoplasmic trafficking, and virus particle production in single cells. We show that the HIV-1 RRE regulates unique, en masse, Rev- and CRM1-dependent "burst-like" transitions of mRNAs from the nucleus to flood the cytoplasm in a non-localized fashion. By contrast, the CTE derived from Mason-Pfizer monkey virus (M-PMV) links gRNAs to microtubules in the cytoplasm, driving them to cluster markedly to the centrosome that forms the pericentriolar core of the microtubule-organizing center (MTOC). Adding each export element to selected heterologous mRNAs was sufficient to confer each distinct export behavior, as was directing Rev/CRM1 or NXF1/NXT1 transport modules to mRNAs using a site-specific RNA tethering strategy. Moreover, multiple CTEs per transcript enhanced MTOC targeting, suggesting that a cooperative mechanism links NXF1/NXT1 to microtubules. Combined, these results reveal striking, unexpected features of retroviral gRNA nucleocytoplasmic transport and demonstrate roles for mRNA export elements that extend beyond nuclear pores to impact gRNA distribution in the cytoplasm.
Collapse
|
106
|
Wynn JE, Zhang W, Tebit DM, Gray LR, Hammarskjold ML, Rekosh D, Santos WL. Characterization and in vitro activity of a branched peptide boronic acid that interacts with HIV-1 RRE RNA. Bioorg Med Chem 2016; 24:3947-3952. [PMID: 27091070 DOI: 10.1016/j.bmc.2016.04.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 04/01/2016] [Accepted: 04/04/2016] [Indexed: 01/10/2023]
Abstract
A branched peptide containing multiple boronic acids was found to bind RRE IIB selectively and inhibit HIV-1 p24 capsid production in a dose-dependent manner. Structure-activity relationship studies revealed that branching in the peptide is crucial for the low micromolar binding towards RRE IIB, and the peptide demonstrates selectivity towards RRE IIB in the presence of tRNA. Footprinting studies suggest a binding site on the upper stem and internal loop regions of the RNA, which induces enzymatic cleavage of the internal loops of RRE IIB upon binding.
Collapse
Affiliation(s)
- Jessica E Wynn
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
| | - Wenyu Zhang
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
| | - Denis M Tebit
- Department of Microbiology, Immunology and Cancer Biology, and The Myles H. Thaler Center for Human Retrovirus Research, University of Virginia, Charlottesville, VA 22908, United States
| | - Laurie R Gray
- Department of Microbiology, Immunology and Cancer Biology, and The Myles H. Thaler Center for Human Retrovirus Research, University of Virginia, Charlottesville, VA 22908, United States
| | - Marie-Louise Hammarskjold
- Department of Microbiology, Immunology and Cancer Biology, and The Myles H. Thaler Center for Human Retrovirus Research, University of Virginia, Charlottesville, VA 22908, United States
| | - David Rekosh
- Department of Microbiology, Immunology and Cancer Biology, and The Myles H. Thaler Center for Human Retrovirus Research, University of Virginia, Charlottesville, VA 22908, United States
| | - Webster L Santos
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States.
| |
Collapse
|
107
|
Choi JS, Han SH, Kim H, Lim YB. Cyclic Peptide-Decorated Self-Assembled Nanohybrids for Selective Recognition and Detection of Multivalent RNAs. Bioconjug Chem 2016; 27:799-808. [PMID: 26886413 DOI: 10.1021/acs.bioconjchem.6b00017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although there has been substantial advancement in the development of nanostructures, the development of self-assembled nanostructures that can selectively recognize multivalent targets has been very difficult. Here we show the proof of concept that topology-controlled peptide nanoassemblies can selectively recognize and detect a multivalent RNA target. We compared the differential behaviors of peptides in a linear or cyclic topology in terms of peptide-gold nanoparticle hybrid nanostructure formation, conformational stabilization, monovalent and multivalent RNA binding in vitro, and multivalent RNA recognition in live cells. When the topology-dependent selectivity amplification of the cyclic peptide hybrids is combined with the noninvasive nature of dark-field microscopy, the cellular localization of the viral Rev response element (RRE) RNA can be monitored in situ. Because intracellular interactions are often mediated by overlapping binding partners with weak affinity, the topology-controlled peptide assemblies can provide a versatile means to convert weak ligands into multivalent ligands with high affinity and selectivity.
Collapse
Affiliation(s)
- Jun Shik Choi
- Translational Research Center for Protein Function Control and Department of Materials Science and Engineering, Yonsei University , Seoul 03722, Korea
| | - So-hee Han
- Translational Research Center for Protein Function Control and Department of Materials Science and Engineering, Yonsei University , Seoul 03722, Korea
| | - Hyoseok Kim
- Translational Research Center for Protein Function Control and Department of Materials Science and Engineering, Yonsei University , Seoul 03722, Korea
| | - Yong-Beom Lim
- Translational Research Center for Protein Function Control and Department of Materials Science and Engineering, Yonsei University , Seoul 03722, Korea
| |
Collapse
|
108
|
Fernandes JD, Booth DS, Frankel AD. A structurally plastic ribonucleoprotein complex mediates post-transcriptional gene regulation in HIV-1. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:470-86. [PMID: 26929078 DOI: 10.1002/wrna.1342] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 01/12/2016] [Accepted: 01/14/2016] [Indexed: 01/28/2023]
Abstract
HIV replication requires the nuclear export of essential, intron-containing viral RNAs. To facilitate export, HIV encodes the viral accessory protein Rev which binds unspliced and partially spliced viral RNAs and creates a ribonucleoprotein complex that recruits the cellular Chromosome maintenance factor 1 export machinery. Exporting RNAs in this manner bypasses the necessity for complete splicing as a prerequisite for mRNA export, and allows intron-containing RNAs to reach the cytoplasm intact for translation and virus packaging. Recent structural studies have revealed that this entire complex exhibits remarkable plasticity at many levels of organization, including RNA folding, protein-RNA recognition, multimer formation, and host factor recruitment. In this review, we explore each aspect of plasticity from structural, functional, and possible therapeutic viewpoints. WIREs RNA 2016, 7:470-486. doi: 10.1002/wrna.1342 For further resources related to this article, please visit the WIREs website.
Collapse
Affiliation(s)
- Jason D Fernandes
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - David S Booth
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Alan D Frankel
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| |
Collapse
|
109
|
Meena CK, Borkotoky S, Murali A. Insight into virus encapsulation mechanism through in silico interaction study between coat protein and RNA operator loops of Sesbania mosaic virus. MOLECULAR BIOSYSTEMS 2016; 12:1996-2009. [DOI: 10.1039/c6mb00206d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Viruses are parasite by nature and they are responsible for many diseases. Inhibitor development is very difficult for viruses due to their rapid mutative nature.
Collapse
Affiliation(s)
- Chetan Kumar Meena
- Centre for Bioinformatics
- School of Life Sciences
- Pondicherry University
- Puducherry - 605 014
- India
| | - Subhomoi Borkotoky
- Centre for Bioinformatics
- School of Life Sciences
- Pondicherry University
- Puducherry - 605 014
- India
| | - Ayaluru Murali
- Centre for Bioinformatics
- School of Life Sciences
- Pondicherry University
- Puducherry - 605 014
- India
| |
Collapse
|
110
|
Tanamura S, Terakado H, Harada K. Cooperative dimerization of a stably folded protein directed by a flexible RNA in the assembly of the HIV Rev dimer-RRE stem II complex. J Mol Recognit 2015; 29:199-209. [PMID: 26620599 DOI: 10.1002/jmr.2518] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 10/13/2015] [Accepted: 10/17/2015] [Indexed: 11/08/2022]
Abstract
The binding of the HIV-1 Rev protein as an oligomer to a viral RNA element, the Rev-response element (RRE), mediates nuclear export of genomic RNA. Assembly of the Rev-RRE ribonucleoprotein (RNP) complex is nucleated by the binding of the first Rev molecule to stem IIB of the RRE. This is followed by stepwise addition of a total of ~six Rev molecules along the RRE through a combination of RNA-protein and protein-protein interactions. RRE stem II, which forms a three-way junction consisting of stems IIA, IIB and IIC, has been shown to bind to two Rev molecules in a cooperative manner, with the second Rev molecule binding to the junction region of stem II. The results of base substitutions at the stem II junction, and characterization of stem II junction variants selected from a randomized library showed that an "open" flexible structure is preferred for binding of the second Rev molecule, and that binding of the second Rev molecule to the junction region is not sequence-specific. Alanine substitutions of a number of Rev amino acid residues implicated to be important for Rev folding in previous structural studies were found to result in a dramatic decrease in the binding of the second Rev molecule. These results support the model that proper folding of Rev is critical in ensuring that the flexible RRE is able to correctly position Rev molecules for specific RNP assembly, and suggests that targeting Rev folding may be effective in the inhibition of Rev function.
Collapse
Affiliation(s)
- Satoshi Tanamura
- Department of Life Sciences, Tokyo Gakugei University, Koganei, Tokyo, 184-8501, Japan
| | - Hiroto Terakado
- Department of Life Sciences, Tokyo Gakugei University, Koganei, Tokyo, 184-8501, Japan
| | - Kazuo Harada
- Department of Life Sciences, Tokyo Gakugei University, Koganei, Tokyo, 184-8501, Japan
| |
Collapse
|
111
|
Remion A, Delord M, Hance AJ, Saragosti S, Mammano F. Kinetics of the establishment of HIV-1 viral interference and comprehensive analysis of the contribution of viral genes. Virology 2015; 487:59-67. [PMID: 26499042 DOI: 10.1016/j.virol.2015.09.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 07/01/2015] [Accepted: 09/26/2015] [Indexed: 10/22/2022]
Abstract
Viral interference defines the reduced susceptibility of an infected cell to reinfection. For HIV-1, both receptor-dependent and independent pathways were described. The relative importance of different receptor-independent pathways has not been addressed. We have used reporter viruses to quantify the percentage of single- and double-infected cells, as a function of the delay between the two infections. For co-infection experiments, the frequency of double infected cells was higher than expected for independent events. By delaying the second infection, this frequency progressively diminished, resulting in significant interference after 18h. Interference measured here was largely receptor-independent. By individually deleting viral genes or expressing them in isolation, we demonstrate that the viral protein Rev plays a dominant role, while other viral proteins contributes to optimal interference. Our study defines the kinetics of early HIV-1 interference, describing the transition from higher susceptibility to double-infection to viral interference, and identifies Rev as its dominant effector.
Collapse
Affiliation(s)
- Azaria Remion
- INSERM, U941, Paris, France; Univ Paris Diderot, Sorbonne Paris Cité, Paris, France; Institut Universitaire d'Hématologie, Hôpital Saint-Louis, Paris, France
| | - Marc Delord
- Univ Paris Diderot, Sorbonne Paris Cité, Paris, France; Institut Universitaire d'Hématologie, Hôpital Saint-Louis, Paris, France
| | - Allan J Hance
- INSERM, U941, Paris, France; Univ Paris Diderot, Sorbonne Paris Cité, Paris, France; Institut Universitaire d'Hématologie, Hôpital Saint-Louis, Paris, France
| | - Sentob Saragosti
- INSERM, U941, Paris, France; Univ Paris Diderot, Sorbonne Paris Cité, Paris, France; Institut Universitaire d'Hématologie, Hôpital Saint-Louis, Paris, France
| | - Fabrizio Mammano
- INSERM, U941, Paris, France; Univ Paris Diderot, Sorbonne Paris Cité, Paris, France; Institut Universitaire d'Hématologie, Hôpital Saint-Louis, Paris, France.
| |
Collapse
|
112
|
Jayaraman B, Mavor D, Gross JD, Frankel AD. Thermodynamics of Rev-RNA interactions in HIV-1 Rev-RRE assembly. Biochemistry 2015; 54:6545-54. [PMID: 26422686 DOI: 10.1021/acs.biochem.5b00876] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The HIV-1 protein Rev facilitates the nuclear export of intron-containing viral mRNAs by recognizing a structured RNA site, the Rev-response-element (RRE), contained in an intron. Rev assembles as a homo-oligomer on the RRE using its α-helical arginine-rich-motif (ARM) for RNA recognition. One unique feature of this assembly is the repeated use of the ARM from individual Rev subunits to contact distinct parts of the RRE in different binding modes. How the individual interactions differ and how they contribute toward forming a functional complex is poorly understood. Here we examine the thermodynamics of Rev-ARM peptide binding to two sites, RRE stem IIB, the high-affinity site that nucleates Rev assembly, and stem IA, a potential intermediate site during assembly, using NMR spectroscopy and isothermal titration calorimetry (ITC). NMR data indicate that the Rev-IIB complex forms a stable interface, whereas the Rev-IA interface is highly dynamic. ITC studies show that both interactions are enthalpy-driven, with binding to IIB being 20-30 fold tighter than to IA. Salt-dependent decreases in affinity were similar at both sites and predominantly enthalpic in nature, reflecting the roles of electrostatic interactions with arginines. However, the two interactions display strikingly different partitioning between enthalpy and entropy components, correlating well with the NMR observations. Our results illustrate how the variation in binding modes to different RRE target sites may influence the stability or order of Rev-RRE assembly and disassembly, and consequently its function.
Collapse
Affiliation(s)
- Bhargavi Jayaraman
- Department of Biochemistry and Biophysics and ‡Department of Pharmaceutical Chemistry, University of California , San Francisco, United States
| | - David Mavor
- Department of Biochemistry and Biophysics and ‡Department of Pharmaceutical Chemistry, University of California , San Francisco, United States
| | - John D Gross
- Department of Biochemistry and Biophysics and ‡Department of Pharmaceutical Chemistry, University of California , San Francisco, United States
| | - Alan D Frankel
- Department of Biochemistry and Biophysics and ‡Department of Pharmaceutical Chemistry, University of California , San Francisco, United States
| |
Collapse
|
113
|
Smith C, Tu LC, Grunwald D. A 4D view on mRNA. Oncotarget 2015; 6:28515-6. [PMID: 26387129 PMCID: PMC4745664 DOI: 10.18632/oncotarget.5121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Carlas Smith
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA USA
| | - Li-Chun Tu
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA USA
| | - David Grunwald
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA USA.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA USA
| |
Collapse
|
114
|
Inhibition of HIV-1 assembly by coiled-coil domain containing protein 8 in human cells. Sci Rep 2015; 5:14724. [PMID: 26423533 PMCID: PMC4589731 DOI: 10.1038/srep14724] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 09/03/2015] [Indexed: 12/22/2022] Open
Abstract
Human Immunodeficiency Virus type 1 (HIV-1) major structure protein Gag is synthesized in the cytoplasm, assembles on the plasma membrane, subsequently buds and releases. HIV-1 viral particles incorporate a number of host proteins to facilitate or inhibit HIV-1 replication. Here we identify a new host protein, coiled-coil domain containing protein 8 (CCDC8), in HIV-1 particles. Incorporation of CCDC8 into virions is dependent on the interaction between CCDC8 and Gag matrix region. Exogenous overexpression of CCDC8 can strongly inhibit HIV-1 production, up to ~30 fold. CCDC8 is a membrane-associated protein. The interaction between exogenously expressed CCDC8 and Gag on the plasma membrane changes the assembly of Gag, and redirects it into intracellular sites, or causes Gag endocytosis. CCDC8, along with cytoskeleton protein obscuring-like1 (Obsl1) and E3 ligase Cul7, induces Gag polyubiquitination and degradation. Thus we identify a new host protein and a new pathway for HIV-1 Gag polyubiquitination and degradation. This pathway presents potential therapeutic strategies against HIV infection.
Collapse
|
115
|
Zhong F, Geng G, Chen B, Pan T, Li Q, Zhang H, Bai C. Identification of benzenesulfonamide quinoline derivatives as potent HIV-1 replication inhibitors targeting Rev protein. Org Biomol Chem 2015; 13:1792-9. [PMID: 25503645 DOI: 10.1039/c4ob02247e] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Human immunodeficiency virus type 1 (HIV-1) Rev protein facilitates the export of viral RNA from nucleus to cytoplasm, which is a key step in HIV-1 pathogenesis and transmission. In this study, we have screened a commercial library and identified the hit compound 1 bearing a benzenesulfonamide quinoline scaffold that inhibited Rev activity and HIV-1 infectivity. Compounds bearing this scaffold were synthesized and their SAR was studied. We identified compound 20 with low toxicity and potent activity to inhibit HIV-1 replication by affecting Rev function.
Collapse
Affiliation(s)
- Fudi Zhong
- Institute of Human Virology, Key Laboratory of Tropical Diseases Control of Ministry of Education of China, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
| | | | | | | | | | | | | |
Collapse
|
116
|
Sherrill-Mix S, Ocwieja KE, Bushman FD. Gene activity in primary T cells infected with HIV89.6: intron retention and induction of genomic repeats. Retrovirology 2015; 12:79. [PMID: 26377088 PMCID: PMC4574318 DOI: 10.1186/s12977-015-0205-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 08/28/2015] [Indexed: 02/07/2023] Open
Abstract
Background HIV infection has been reported to alter cellular gene activity, but published studies have commonly assayed transformed cell lines and lab-adapted HIV strains, yielding inconsistent results. Here we carried out a deep RNA-Seq analysis of primary human T cells infected with the low passage HIV isolate HIV89.6. Results Seventeen percent of cellular genes showed altered activity 48 h after infection. In a meta-analysis including four other studies, our data differed from studies of HIV infection in cell lines but showed more parallels with infections of primary cells. We found a global trend toward retention of introns after infection, suggestive of a novel cellular response to infection. HIV89.6 infection was also associated with activation of several human endogenous retroviruses (HERVs) and retrotransposons, of interest as possible novel antigens that could serve as vaccine targets. The most highly activated group of HERVs was a subset of the ERV-9. Analysis showed that activation was associated with a particular variant of ERV-9 long terminal repeats that contains an indel near the U3-R border. These data also allowed quantification of >70 splice forms of the HIV89.6 RNA and specified the main types of chimeric HIV89.6-host RNAs. Comparison to over 100,000 integration site sequences from the same infected cell populations allowed quantification of authentic versus artifactual chimeric reads, showing that 5′ read-in, splicing out of HIV89.6 from the D4 donor and 3′ read-through were the most common HIV89.6-host cell chimeric RNA forms. Conclusions Analysis of RNA abundance after infection of primary T cells with the low passage HIV89.6 isolate disclosed multiple novel features of HIV-host interactions, notably intron retention and induction of transcription of retrotransposons and endogenous retroviruses. Electronic supplementary material The online version of this article (doi:10.1186/s12977-015-0205-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Scott Sherrill-Mix
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, 425 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA, 19104, USA.
| | - Karen E Ocwieja
- Children's Hospital of Philadelphia, 3401 Civic Center Blvd., Philadelphia, PA, 19104, USA.
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, 425 Johnson Pavilion, 3610 Hamilton Walk, Philadelphia, PA, 19104, USA.
| |
Collapse
|
117
|
Huang F, Zhang J, Zhang Y, Geng G, Liang J, Li Y, Chen J, Liu C, Zhang H. RNA helicase MOV10 functions as a co-factor of HIV-1 Rev to facilitate Rev/RRE-dependent nuclear export of viral mRNAs. Virology 2015; 486:15-26. [PMID: 26379090 DOI: 10.1016/j.virol.2015.08.026] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 08/20/2015] [Accepted: 08/25/2015] [Indexed: 12/25/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) exploits multiple host factors during its replication. The REV/RRE-dependent nuclear export of unspliced/partially spliced viral transcripts needs the assistance of host proteins. Recent studies have shown that MOV10 overexpression inhibited HIV-1 replication at various steps. However, the endogenous MOV10 was required in certain step(s) of HIV-1 replication. In this report, we found that MOV10 potently enhances the nuclear export of viral mRNAs and subsequently increases the expression of Gag protein and other late products through affecting the Rev/RRE axis. The co-immunoprecipitation analysis indicated that MOV10 interacts with Rev in an RNA-independent manner. The DEAG-box of MOV10 was required for the enhancement of Rev/RRE-dependent nuclear export and the DEAG-box mutant showed a dominant-negative activity. Our data propose that HIV-1 utilizes the anti-viral factor MOV10 to function as a co-factor of Rev and demonstrate the complicated effects of MOV10 on HIV-1 life cycle.
Collapse
Affiliation(s)
- Feng Huang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Junsong Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Yijun Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Guannan Geng
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Juanran Liang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Yingniang Li
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Jingliang Chen
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Chao Liu
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.
| | - Hui Zhang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| |
Collapse
|
118
|
Boons E, Vanstreels E, Jacquemyn M, Nogueira TC, Neggers JE, Vercruysse T, van den Oord J, Tamir S, Shacham S, Landesman Y, Snoeck R, Pannecouque C, Andrei G, Daelemans D. Human Exportin-1 is a Target for Combined Therapy of HIV and AIDS Related Lymphoma. EBioMedicine 2015; 2:1102-13. [PMID: 26501108 PMCID: PMC4588406 DOI: 10.1016/j.ebiom.2015.07.041] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 07/29/2015] [Accepted: 07/29/2015] [Indexed: 11/12/2022] Open
Abstract
Infection with HIV ultimately leads to advanced immunodeficiency resulting in an increased incidence of cancer. For example primary effusion lymphoma (PEL) is an aggressive non-Hodgkin lymphoma with very poor prognosis that typically affects HIV infected individuals in advanced stages of immunodeficiency. Here we report on the dual anti-HIV and anti-PEL effect of targeting a single process common in both diseases. Inhibition of the exportin-1 (XPO1) mediated nuclear transport by clinical stage orally bioavailable small molecule inhibitors (SINE) prevented the nuclear export of the late intron-containing HIV RNA species and consequently potently suppressed viral replication. In contrast, in CRISPR-Cas9 genome edited cells expressing mutant C528S XPO1, viral replication was unaffected upon treatment, clearly demonstrating the anti-XPO1 mechanism of action. At the same time, SINE caused the nuclear accumulation of p53 tumor suppressor protein as well as inhibition of NF-κB activity in PEL cells resulting in cell cycle arrest and effective apoptosis induction. In vivo, oral administration arrested PEL tumor growth in engrafted mice. Our findings provide strong rationale for inhibiting XPO1 as an innovative strategy for the combined anti-retroviral and anti-neoplastic treatment of HIV and PEL and offer perspectives for the treatment of other AIDS-associated cancers and potentially other virus-related malignancies.
Collapse
MESH Headings
- Acrylates/chemistry
- Acrylates/pharmacology
- Acrylates/therapeutic use
- Active Transport, Cell Nucleus/drug effects
- Animals
- Apoptosis/drug effects
- Base Sequence
- CRISPR-Cas Systems/genetics
- Cell Cycle Checkpoints/drug effects
- Cell Line
- Cell Nucleus/drug effects
- Cell Nucleus/metabolism
- Female
- HIV/drug effects
- HIV/isolation & purification
- Humans
- Karyopherins/antagonists & inhibitors
- Karyopherins/metabolism
- Lymphoma, AIDS-Related/drug therapy
- Mice, Nude
- Molecular Sequence Data
- Molecular Targeted Therapy
- NF-kappa B/metabolism
- Protein Binding/drug effects
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Viral/metabolism
- Receptors, Cytoplasmic and Nuclear/antagonists & inhibitors
- Receptors, Cytoplasmic and Nuclear/metabolism
- Reproducibility of Results
- Triazoles/chemistry
- Triazoles/pharmacology
- Triazoles/therapeutic use
- Tumor Suppressor Protein p53/metabolism
- Virus Replication/drug effects
- Xenograft Model Antitumor Assays
- rev Gene Products, Human Immunodeficiency Virus/genetics
- rev Gene Products, Human Immunodeficiency Virus/metabolism
- Exportin 1 Protein
Collapse
Affiliation(s)
- Eline Boons
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, B-3000 Leuven, Belgium
| | - Els Vanstreels
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, B-3000 Leuven, Belgium
| | - Maarten Jacquemyn
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, B-3000 Leuven, Belgium
| | - Tatiane C. Nogueira
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, B-3000 Leuven, Belgium
| | - Jasper E. Neggers
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, B-3000 Leuven, Belgium
| | - Thomas Vercruysse
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, B-3000 Leuven, Belgium
| | - Joost van den Oord
- KU Leuven, Department of Imaging and Pathology, Translational Cell & Tissue Research, B-3000 Leuven, Belgium
| | | | | | | | - Robert Snoeck
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, B-3000 Leuven, Belgium
| | - Christophe Pannecouque
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, B-3000 Leuven, Belgium
| | - Graciela Andrei
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, B-3000 Leuven, Belgium
| | - Dirk Daelemans
- KU Leuven, Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, B-3000 Leuven, Belgium
| |
Collapse
|
119
|
Nkeze J, Li L, Benko Z, Li G, Zhao RY. Molecular characterization of HIV-1 genome in fission yeast Schizosaccharomyces pombe. Cell Biosci 2015; 5:47. [PMID: 26309721 PMCID: PMC4549081 DOI: 10.1186/s13578-015-0037-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 07/27/2015] [Indexed: 11/25/2022] Open
Abstract
Background The human immunodeficiency virus type 1 (HIV-1) genome (~9 kb RNA) is flanked by two long terminal repeats (LTR) promoter regions with nine open reading frames, which encode Gag, Pol and Env polyproteins, four accessory proteins (Vpu, Vif, Vpr, Nef) and two regulatory proteins (Rev, Tat). In this study, we carried out a genome-wide and functional analysis of the HIV-1 genome in fission yeast (Schizosaccharomyces pombe). Results Each one of the HIV-1 genes was cloned and expressed individually in fission yeast. Subcellular localization of each viral protein was first examined. The effect of protein expression on cellular proliferation and colony formations, an indication of cytotoxicity, were observed. Overall, there is a general correlation of subcellular localization of each viral protein between fission yeast and mammalian cells. Three viral proteins, viral protein R (Vpr), protease (PR) and regulator of expression of viral protein (Rev), were found to inhibit cellular proliferation. Rev was chosen for further analysis in fission yeast and mammalian cells. Consistent with the observation in fission yeast, expression of HIV-1 rev gene also caused growth retardation in mammalian cells. However, the observed growth delay was neither due to the cytotoxic effect nor due to alterations in cell cycling. Mechanistic testing of the Rev effect suggests it triggers transient induction of cellular oxidative stress. Conclusions Some of the behavioral and functional similarities of Rev between fission yeast and mammalian cells suggest fission yeast might be a useful model system for further studies of molecular functions of Rev and other HIV-1 viral proteins.
Collapse
Affiliation(s)
- Joseph Nkeze
- Division of Molecular Pathology, Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201-1192 USA
| | - Lin Li
- Division of Molecular Pathology, Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201-1192 USA.,AIDS Research Department, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071 China
| | - Zsigmond Benko
- Division of Molecular Pathology, Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201-1192 USA.,Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Ge Li
- Division of Molecular Pathology, Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201-1192 USA
| | - Richard Y Zhao
- Division of Molecular Pathology, Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201-1192 USA.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201-1192 USA.,Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201-1192 USA
| |
Collapse
|
120
|
Rojas-Araya B, Ohlmann T, Soto-Rifo R. Translational Control of the HIV Unspliced Genomic RNA. Viruses 2015; 7:4326-51. [PMID: 26247956 PMCID: PMC4576183 DOI: 10.3390/v7082822] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 05/18/2015] [Accepted: 07/17/2015] [Indexed: 01/16/2023] Open
Abstract
Post-transcriptional control in both HIV-1 and HIV-2 is a highly regulated process that commences in the nucleus of the host infected cell and finishes by the expression of viral proteins in the cytoplasm. Expression of the unspliced genomic RNA is particularly controlled at the level of RNA splicing, export, and translation. It appears increasingly obvious that all these steps are interconnected and they result in the building of a viral ribonucleoprotein complex (RNP) that must be efficiently translated in the cytosolic compartment. This review summarizes our knowledge about the genesis, localization, and expression of this viral RNP.
Collapse
Affiliation(s)
- Bárbara Rojas-Araya
- Molecular and Cellular Virology Laboratory, Program of Virology, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Independencia 834100, Santiago, Chile.
| | - Théophile Ohlmann
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon 69007, France.
- Inserm, U1111, Lyon 69007, France.
- Ecole Normale Supérieure de Lyon, Lyon 69007, France.
- Université Lyon 1, Centre International de Recherche en Infectiologie, Lyon 69007, France.
- CNRS, UMR5308, Lyon 69007, France.
| | - Ricardo Soto-Rifo
- Molecular and Cellular Virology Laboratory, Program of Virology, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Independencia 834100, Santiago, Chile.
| |
Collapse
|
121
|
Abstract
The discovery of long non-coding RNAs (lncRNAs) and the elucidation of the mechanisms by which they affect different disease states are providing researchers with a better understanding of a wide array of disease pathways. Moreover, lncRNAs are presenting themselves as both unique diagnostic biomarkers as well as novel targets against which to develop new therapeutics. Here we will explore the intricate network of non-coding RNAs associated with infection by the human immunodeficiency virus (HIV). Non-coding RNAs derived from both the human host as well as those from HIV itself are emerging as important regulatory elements. We discuss here the various mechanisms through which both small and long non-coding RNAs impact viral replication, pathogenesis and disease progression. Given the lack of an effective vaccine or cure for HIV and the scale of the current pandemic, a deeper understanding of the complex interplay between non-coding RNAs and HIV will support the development of innovative strategies for the treatment of HIV/acquired immunodeficiency disease (AIDS).
Collapse
Affiliation(s)
- Daniel C Lazar
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA.
| | - Kevin V Morris
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA; School of Biotechnology and Biomedical Sciences, University of New South Wales, Kensington, NSW, Australia.
| | - Sheena M Saayman
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA.
| |
Collapse
|
122
|
HIV Rev Assembly on the Rev Response Element (RRE): A Structural Perspective. Viruses 2015; 7:3053-75. [PMID: 26075509 PMCID: PMC4488727 DOI: 10.3390/v7062760] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 06/05/2015] [Indexed: 01/18/2023] Open
Abstract
HIV-1 Rev is an ~13 kD accessory protein expressed during the early stage of virus replication. After translation, Rev enters the nucleus and binds the Rev response element (RRE), a ~350 nucleotide, highly structured element embedded in the env gene in unspliced and singly spliced viral RNA transcripts. Rev-RNA assemblies subsequently recruit Crm1 and other cellular proteins to form larger complexes that are exported from the nucleus. Once in the cytoplasm, the complexes dissociate and unspliced and singly-spliced viral RNAs are packaged into nascent virions or translated into viral structural proteins and enzymes, respectively. Rev binding to the RRE is a complex process, as multiple copies of the protein assemble on the RNA in a coordinated fashion via a series of Rev-Rev and Rev-RNA interactions. Our understanding of the nature of these interactions has been greatly advanced by recent studies using X-ray crystallography, small angle X-ray scattering (SAXS) and single particle electron microscopy as well as biochemical and genetic methodologies. These advances are discussed in detail in this review, along with perspectives on development of antiviral therapies targeting the HIV-1 RRE.
Collapse
|
123
|
Wynn JE, Santos WL. HIV-1 drug discovery: targeting folded RNA structures with branched peptides. Org Biomol Chem 2015; 13:5848-58. [PMID: 25958855 PMCID: PMC4511164 DOI: 10.1039/c5ob00589b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Human immunodeficiency virus type 1 (HIV-1) is an RNA virus that is prone to high rates of mutation. While the disease is managed with current antiretroviral therapies, drugs with a new mode of action are needed. A strategy towards this goal is aimed at targeting the native three-dimensional fold of conserved RNA structures. This perspective highlights medium-sized peptides and peptidomimetics used to target two conserved RNA structures of HIV-1. In particular, branched peptides have the capacity to bind in a multivalent fashion, utilizing a large surface area to achieve the necessary affinity and selectivity toward the target RNA.
Collapse
Affiliation(s)
- Jessica E Wynn
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, USA.
| | | |
Collapse
|
124
|
Faust O, Bigman L, Friedler A. A role of disordered domains in regulating protein oligomerization and stability. Chem Commun (Camb) 2015; 50:10797-800. [PMID: 25054624 DOI: 10.1039/c4cc03863k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Intrinsically disordered proteins (IDPs) or regions (IDRs) in proteins hold many functions but their biological roles are still not fully understood. Here we describe a new role of such regions. Using the HIV-1 Rev protein, we show that disordered domains have a role in maintaining the correct oligomeric state and the thermodynamic stability of proteins.
Collapse
Affiliation(s)
- Ofrah Faust
- Institute of Chemistry, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, Givat Ram 91904, Jerusalem, Israel.
| | | | | |
Collapse
|
125
|
Platt C, Calimano M, Nemet J, Bubenik J, Cochrane A. Differential Effects of Tra2ß Isoforms on HIV-1 RNA Processing and Expression. PLoS One 2015; 10:e0125315. [PMID: 25970345 PMCID: PMC4430212 DOI: 10.1371/journal.pone.0125315] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 03/16/2015] [Indexed: 12/03/2022] Open
Abstract
Balanced processing of HIV-1 RNA is critical to virus replication and is regulated by host factors. In this report, we demonstrate that overexpression of either Tra2α or Tra2β results in a marked reduction in HIV-1 Gag/ Env expression, an effect associated with changes in HIV-1 RNA accumulation, altered viral splice site usage, and a block to export of HIV-1 genomic RNA. A natural isoform of Tra2β (Tra2ß3), lacking the N-terminal RS domain, also suppressed HIV-1 expression but had different effects on viral RNA processing. The functional differences between the Tra2β isoforms were also observed in the context of another RNA substrate indicating that these factors have distinct functions within the cell. Finally, we demonstrate that Tra2ß depletion results in a selective reduction in HIV-1 Env expression as well as an increase in multiply spliced viral RNA. Together, the findings indicate that Tra2α/β can play important roles in regulating HIV-1 RNA metabolism and expression.
Collapse
MESH Headings
- Gene Expression Regulation
- HEK293 Cells
- HIV-1/genetics
- HIV-1/metabolism
- HeLa Cells
- Host-Pathogen Interactions
- Humans
- Nerve Tissue Proteins/antagonists & inhibitors
- Nerve Tissue Proteins/genetics
- Nerve Tissue Proteins/metabolism
- Protein Isoforms/antagonists & inhibitors
- Protein Isoforms/genetics
- Protein Isoforms/metabolism
- RNA Splice Sites
- RNA Splicing
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- RNA, Viral/genetics
- RNA, Viral/metabolism
- RNA-Binding Proteins/antagonists & inhibitors
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Serine-Arginine Splicing Factors
- Signal Transduction
- Virus Replication
- env Gene Products, Human Immunodeficiency Virus/antagonists & inhibitors
- env Gene Products, Human Immunodeficiency Virus/genetics
- env Gene Products, Human Immunodeficiency Virus/metabolism
- gag Gene Products, Human Immunodeficiency Virus/antagonists & inhibitors
- gag Gene Products, Human Immunodeficiency Virus/genetics
- gag Gene Products, Human Immunodeficiency Virus/metabolism
Collapse
Affiliation(s)
- Craig Platt
- Dept. of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Maria Calimano
- Dept. of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Josip Nemet
- Dept. of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jodi Bubenik
- Dept. of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Alan Cochrane
- Dept. of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
| |
Collapse
|
126
|
Campos N, Myburgh R, Garcel A, Vautrin A, Lapasset L, Nadal ES, Mahuteau-Betzer F, Najman R, Fornarelli P, Tantale K, Basyuk E, Séveno M, Venables JP, Pau B, Bertrand E, Wainberg MA, Speck RF, Scherrer D, Tazi J. Long lasting control of viral rebound with a new drug ABX464 targeting Rev - mediated viral RNA biogenesis. Retrovirology 2015; 12:30. [PMID: 25889234 PMCID: PMC4422473 DOI: 10.1186/s12977-015-0159-3] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 03/24/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Current therapies have succeeded in controlling AIDS pandemic. However, there is a continuing need for new drugs, in particular those acting through new and as yet unexplored mechanisms of action to achieve HIV infection cure. We took advantage of the unique feature of proviral genome to require both activation and inhibition of splicing of viral transcripts to develop molecules capable of achieving long lasting effect on viral replication in humanized mouse models through inhibition of Rev-mediated viral RNA biogenesis. RESULTS Current HIV therapies reduce viral load during treatment but titers rebound after treatment is discontinued. We devised a new drug that has a long lasting effect after viral load reduction. We demonstrate here that ABX464 compromises HIV replication of clinical isolates of different subtypes without selecting for drug resistance in PBMCs or macrophages. ABX464 alone, also efficiently compromised viral proliferation in two humanized mouse models infected with HIV that require a combination of 3TC, Raltegravir and Tenofovir (HAART) to achieve viral inhibition in current protocols. Crucially, while viral load increased dramatically just one week after stopping HAART treatment, only slight rebound was observed following treatment cessation with ABX464 and the magnitude of the rebound was maintained below to that of HAART for two months after stopping the treatment. Using a system to visualize single HIV RNA molecules in living cells, we show that ABX464 inhibits viral replication by preventing Rev-mediated export of unspliced HIV-1 transcripts to the cytoplasm and by interacting with the Cap Binding Complex (CBC). Deep sequencing of viral RNA from treated cells established that retained viral RNA is massively spliced but importantly, normal cellular splicing is unaffected by the drug. Consistently ABX464 is non-toxic in humans and therefore represents a promising complement to current HIV therapies. CONCLUSIONS ABX464 represents a novel class of anti-HIV molecules with unique properties. ABX464 has a long lasting effect in humanized mice and neutralizes the expression of HIV-1 proviral genome of infected immune cells including reservoirs and it is therefore a promising drug toward a functional cure of HIV.
Collapse
Affiliation(s)
- Noëlie Campos
- ABIVAX, 1919 route de Mende, 34293, Montpellier Cedex 5, France.
| | - Renier Myburgh
- Division of Infectious Diseases and Hospital Epidemiology Department of Internal Medicin, University of Zurich, University Hospital, Raemistrasse 100, 8091, Zurich, Switzerland.
| | - Aude Garcel
- ABIVAX, 1919 route de Mende, 34293, Montpellier Cedex 5, France.
| | - Audrey Vautrin
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS UMR 5535, 1919 route de Mende, 34293, Montpellier Cedex 5, France.
| | - Laure Lapasset
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS UMR 5535, 1919 route de Mende, 34293, Montpellier Cedex 5, France.
| | - Erika Schläpfer Nadal
- Division of Infectious Diseases and Hospital Epidemiology Department of Internal Medicin, University of Zurich, University Hospital, Raemistrasse 100, 8091, Zurich, Switzerland.
| | - Florence Mahuteau-Betzer
- Institut Curie, CNRS UMR9187, INSERM U1196, Centre universitaire, Bâtiment 110, 15 rue Georges Clémenceau, 91405, ORSAY CEDEX, France.
| | - Romain Najman
- ABIVAX, 1919 route de Mende, 34293, Montpellier Cedex 5, France.
| | | | - Katjana Tantale
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS UMR 5535, 1919 route de Mende, 34293, Montpellier Cedex 5, France.
| | - Eugénia Basyuk
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS UMR 5535, 1919 route de Mende, 34293, Montpellier Cedex 5, France.
| | - Martial Séveno
- Plate-forme de Protéomique Fonctionnelle (FPP) IGF, UMR 5203 CNRS - INSERM U661- UM, 141 rue de la Cardonille (pièce 029), 34094, Montpellier CEDEX 05, France.
| | - Julian P Venables
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS UMR 5535, 1919 route de Mende, 34293, Montpellier Cedex 5, France.
| | - Bernard Pau
- Université de Montpellier, UFR Pharmacie, 15 Avenue Charles Flahault, 34000, Montpellier, France.
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS UMR 5535, 1919 route de Mende, 34293, Montpellier Cedex 5, France.
| | - Mark A Wainberg
- McGill AIDS Center, Lady Davis Institute - Jewish General Hospital, Montréal, QC, Canada.
| | - Roberto F Speck
- Division of Infectious Diseases and Hospital Epidemiology Department of Internal Medicin, University of Zurich, University Hospital, Raemistrasse 100, 8091, Zurich, Switzerland.
| | - Didier Scherrer
- ABIVAX, 1919 route de Mende, 34293, Montpellier Cedex 5, France.
| | - Jamal Tazi
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS UMR 5535, 1919 route de Mende, 34293, Montpellier Cedex 5, France.
| |
Collapse
|
127
|
Budhiraja S, Liu H, Couturier J, Malovannaya A, Qin J, Lewis DE, Rice AP. Mining the human complexome database identifies RBM14 as an XPO1-associated protein involved in HIV-1 Rev function. J Virol 2015; 89:3557-67. [PMID: 25589658 PMCID: PMC4403413 DOI: 10.1128/jvi.03232-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 01/06/2015] [Indexed: 12/24/2022] Open
Abstract
UNLABELLED By recruiting the host protein XPO1 (CRM1), the HIV-1 Rev protein mediates the nuclear export of incompletely spliced viral transcripts. We mined data from the recently described human nuclear complexome to identify a host protein, RBM14, which associates with XPO1 and Rev and is involved in Rev function. Using a Rev-dependent p24 reporter plasmid, we found that RBM14 depletion decreased Rev activity and Rev-mediated enhancement of the cytoplasmic levels of unspliced viral transcripts. RBM14 depletion also reduced p24 expression during viral infection, indicating that RBM14 is limiting for Rev function. RBM14 has previously been shown to localize to nuclear paraspeckles, a structure implicated in retaining unspliced HIV-1 transcripts for either Rev-mediated nuclear export or degradation. We found that depletion of NEAT1 RNA, a long noncoding RNA required for paraspeckle integrity, abolished the ability of overexpressed RBM14 to enhance Rev function, indicating the dependence of RBM14 function on paraspeckle integrity. Our study extends the known host cell interactome of Rev and XPO1 and further substantiates a critical role for paraspeckles in the mechanism of action of Rev. Our study also validates the nuclear complexome as a database from which viral cofactors can be mined. IMPORTANCE This study mined a database of nuclear protein complexes to identify a cellular protein named RBM14 that is associated with XPO1 (CRM1), a nuclear protein that binds to the HIV-1 Rev protein and mediates nuclear export of incompletely spliced viral RNAs. Functional assays demonstrated that RBM14, a protein found in paraspeckle structures in the nucleus, is involved in HIV-1 Rev function. This study validates the nuclear complexome database as a reference that can be mined to identify viral cofactors.
Collapse
Affiliation(s)
- Sona Budhiraja
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Hongbing Liu
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Jacob Couturier
- Department of Internal Medicine, University of Texas Health Sciences Center, Houston, Texas, USA
| | - Anna Malovannaya
- Department of Biochemistry, Baylor College of Medicine, Houston, Texas, USA
| | - Jun Qin
- Department of Biochemistry, Baylor College of Medicine, Houston, Texas, USA
| | - Dorothy E Lewis
- Department of Internal Medicine, University of Texas Health Sciences Center, Houston, Texas, USA
| | - Andrew P Rice
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| |
Collapse
|
128
|
A mutant tat protein inhibits HIV-1 reverse transcription by targeting the reverse transcription complex. J Virol 2015; 89:4827-36. [PMID: 25673710 DOI: 10.1128/jvi.03440-14] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 02/03/2015] [Indexed: 12/24/2022] Open
Abstract
UNLABELLED Previously, we reported that a mutant of Tat referred to as Nullbasic inhibits HIV-1 reverse transcription although the mechanism of action is unknown. Here we show that Nullbasic is a reverse transcriptase (RT) binding protein that targets the reverse transcription complex rather than directly inhibiting RT activity. An interaction between Nullbasic and RT was observed by using coimmunoprecipitation and pulldown assays, and a direct interaction was measured by using a biolayer interferometry assay. Mixtures of recombinant 6×His-RT and Nullbasic-FLAG-V5-6×His at molar ratios of up to 1:20,000 did not inhibit RT activity in standard homopolymer primer template assays. An analysis of virus made by cells that coexpressed Nullbasic showed that Nullbasic copurified with virus particles, indicating that it was a virion protein. In addition, analysis of reverse transcription complexes (RTCs) isolated from cells infected with wild type or Nullbasic-treated HIV-1 showed that Nullbasic reduced the levels of viral DNA in RTC fractions. In addition, a shift in the distribution of viral DNA and CAp24 to less-dense non-RTC fractions was observed, indicating that RTC activity from Nullbasic-treated virus was impaired. Further analysis showed that viral cores isolated from Nullbasic-treated HIV undergo increased disassembly in vitro compared to untreated HIV-1. To our knowledge, this is the first description of an antiviral protein that inhibits reverse transcription by targeting the RTC and affecting core stability. IMPORTANCE HIV-1 infection is treated by using combinations of antiretroviral drugs that target independent steps of virus replication. A newly described antiviral protein called Nullbasic can also inhibit a combination of different steps in virus replication (transcription, reverse transcription, and Rev-mediated viral mRNA transport), although the precise mechanism of action is unknown. This study shows that Nullbasic can inhibit reverse transcription by binding to the viral enzyme called reverse transcriptase, which results in accelerated uncoating of the viral core and instability of the viral apparatus called the reverse transcription complex (RTC). This unique antiviral activity may inform development of other RTC inhibitors, as well as providing a unique investigative tool for dissecting the RTC cellular composition.
Collapse
|
129
|
Li M. Proteomics in the investigation of HIV-1 interactions with host proteins. Proteomics Clin Appl 2015; 9:221-34. [PMID: 25523935 DOI: 10.1002/prca.201400101] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 11/30/2014] [Accepted: 12/16/2014] [Indexed: 01/09/2023]
Abstract
Productive HIV-1 infection depends on host machinery, including a broad array of cellular proteins. Proteomics has played a significant role in the discovery of HIV-1 host proteins. In this review, after a brief survey of the HIV-1 host proteins that were discovered by proteomic analyses, I focus on analyzing the interactions between the virion and host proteins, as well as the technologies and strategies used in those proteomic studies. With the help of proteomics, the identification and characterization of HIV-1 host proteins can be translated into novel antiretroviral therapeutics.
Collapse
Affiliation(s)
- Ming Li
- Laboratory of Retrovirology, Division of Infectious Diseases, Department of Medicine, Alpert Medical School of Brown University, Providence, RI, USA
| |
Collapse
|
130
|
Takahashi M, Burnett JC, Rossi JJ. Aptamer–siRNA Chimeras for HIV. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 848:211-34. [DOI: 10.1007/978-1-4939-2432-5_11] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
131
|
HIV Latency and the noncoding RNA therapeutic landscape. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 848:169-89. [PMID: 25757621 DOI: 10.1007/978-1-4939-2432-5_9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The Human Immunodeficiency Virus (HIV) belongs to the subfamily of lentiviruses that are characterized by long incubation periods and chronic, persistent infection. The virus integrates into the genome of infected CD4+ cells and, in a subpopulation of cells, adopts a transcriptionally silent state, a process referred to a viral latency. This property makes it exceedingly difficult to therapeutically target the virus and eradicate infection. If left untreated, the inexorable demise of the infected individual's immune system ensues, a causal result of Acquired Immunodeficiency Syndrome (AIDS). Latently infected cells provide a reservoir that maintains viral infection indefinitely. In this chapter we explore the role of noncoding RNAs in HIV infection and in the establishment and maintenance of viral latency. Both short and long noncoding RNAs are endogenous modulators of epigenetic regulation in human cells and play an active role in gene expression. Lastly, we explore therapeutic modalities based on expressed RNAs that are capable of countering infection, transcriptionally regulating the virus, and suppressing or activating the latent state.
Collapse
|
132
|
Umunnakwe CN, Loyd H, Cornick K, Chavez JR, Dobbs D, Carpenter S. Computational modeling suggests dimerization of equine infectious anemia virus Rev is required for RNA binding. Retrovirology 2014; 11:115. [PMID: 25533001 PMCID: PMC4299382 DOI: 10.1186/s12977-014-0115-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 11/27/2014] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The lentiviral Rev protein mediates nuclear export of intron-containing viral RNAs that encode structural proteins or serve as the viral genome. Following translation, HIV-1 Rev localizes to the nucleus and binds its cognate sequence, termed the Rev-responsive element (RRE), in incompletely spliced viral RNA. Rev subsequently multimerizes along the viral RNA and associates with the cellular Crm1 export machinery to translocate the RNA-protein complex to the cytoplasm. Equine infectious anemia virus (EIAV) Rev is functionally homologous to HIV-1 Rev, but shares very little sequence similarity and differs in domain organization. EIAV Rev also contains a bipartite RNA binding domain comprising two short arginine-rich motifs (designated ARM-1 and ARM-2) spaced 79 residues apart in the amino acid sequence. To gain insight into the topology of the bipartite RNA binding domain, a computational approach was used to model the tertiary structure of EIAV Rev. RESULTS The tertiary structure of EIAV Rev was modeled using several protein structure prediction and model quality assessment servers. Two types of structures were predicted: an elongated structure with an extended central alpha helix, and a globular structure with a central bundle of helices. Assessment of models on the basis of biophysical properties indicated they were of average quality. In almost all models, ARM-1 and ARM-2 were spatially separated by >15 Å, suggesting that they do not form a single RNA binding interface on the monomer. A highly conserved canonical coiled-coil motif was identified in the central region of EIAV Rev, suggesting that an RNA binding interface could be formed through dimerization of Rev and juxtaposition of ARM-1 and ARM-2. In support of this, purified Rev protein migrated as a dimer in Blue native gels, and mutation of a residue predicted to form a key coiled-coil contact disrupted dimerization and abrogated RNA binding. In contrast, mutation of residues outside the predicted coiled-coil interface had no effect on dimerization or RNA binding. CONCLUSIONS Our results suggest that EIAV Rev binding to the RRE requires dimerization via a coiled-coil motif to juxtapose two RNA binding motifs, ARM-1 and ARM-2.
Collapse
Affiliation(s)
- Chijioke N Umunnakwe
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA. .,Program in Bioinformatics and Computational Biology, Iowa State University, Ames, IA, 50011, USA.
| | - Hyelee Loyd
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA.
| | - Kinsey Cornick
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA.
| | - Jerald R Chavez
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA.
| | - Drena Dobbs
- Department of Genetics, Developmental and Cell Biology, Iowa State University, Ames, IA, 50011, USA. .,Program in Bioinformatics and Computational Biology, Iowa State University, Ames, IA, 50011, USA.
| | - Susan Carpenter
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA.
| |
Collapse
|
133
|
Likhoshvai VA, Khlebodarova TM, Bazhan SI, Gainova IA, Chereshnev VA, Bocharov GA. Mathematical model of the Tat-Rev regulation of HIV-1 replication in an activated cell predicts the existence of oscillatory dynamics in the synthesis of viral components. BMC Genomics 2014; 15 Suppl 12:S1. [PMID: 25564443 PMCID: PMC4303933 DOI: 10.1186/1471-2164-15-s12-s1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Background The life cycle of human immunodeficiency virus type-1 (HIV-1) makes possible the realization of regulatory strategies that can lead to complex dynamical behavior of the system. We analyze the strategy which is based on two feedback mechanisms, one mediating a positive regulation of the virus replication by Tat protein via the antitermination of the genomic RNAs transcription on TAR (transactivation responsive) element of the proviral DNA and the second mechanism providing a negative regulation of the splicing of the full-length (9 kb) RNAs and incompletely spliced (4 kb) RNAs via their transport from the nucleus to the cytoplasm. Although the existence of these two regulatory feedback loops has been considered in other mathematical models, none of them examined the conditions for the emergence of complex oscillatory patterns in the intracellular dynamics of viral components. Results We developed a mechanistic mathematical model for the Tat-Rev mediated regulation of HIV-1 replication, which considers the activation of proviral DNA transcription, the Tat-specific antitermination of transcription on TAR-element, resulting in the synthesis of the full-length 9 kb RNA, the splicing of the 9 kb RNA down to the 4 kb RNA and the 4 kb RNA to 2 kb RNA, the transport of 2 kb mRNAs from the nucleus to the cytoplasm by the intracellular mechanisms, the multiple binding of the Rev protein to RRE (Rev Response Element) sites on 9 kb and 4 kb RNA resulting in their export to the cytoplasm and the synthesis of Tat and Rev proteins in the cytoplasm followed by their transport into the nucleus. The degradation of all viral proteins and RNAs both in the cytoplasm and the nucleus is described. The model parameters values were derived from the published literature data. The model was used to examine the dynamics of the synthesis of the viral proteins Tat and Rev, the mRNAs under the intracellular conditions specific for activated HIV-1 infected macrophages. In addition, we analyzed alternative hypotheses for the re-cycling of the Rev proteins both in the cytoplasm and the nuclear pore complex. Conclusions The quantitative mathematical model of the Tat-Rev regulation of HIV-1 replication predicts the existence of oscillatory dynamics which depends on the efficacy of the Tat and TAR interaction as well as on the Rev-mediated transport processes. The biological relevance of the oscillatory regimes for the HIV-1 life cycle is discussed.
Collapse
|
134
|
Lin MH, Sivakumaran H, Jones A, Li D, Harper C, Wei T, Jin H, Rustanti L, Meunier FA, Spann K, Harrich D. A HIV-1 Tat mutant protein disrupts HIV-1 Rev function by targeting the DEAD-box RNA helicase DDX1. Retrovirology 2014; 11:121. [PMID: 25496916 PMCID: PMC4271445 DOI: 10.1186/s12977-014-0121-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 12/03/2014] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Previously we described a transdominant negative mutant of the HIV-1 Tat protein, termed Nullbasic, that downregulated the steady state levels of unspliced and singly spliced viral mRNA, an activity caused by inhibition of HIV-1 Rev activity. Nullbasic also altered the subcellular localizations of Rev and other cellular proteins, including CRM1, B23 and C23 in a Rev-dependent manner, suggesting that Nullbasic may disrupt Rev function and trafficking by intervening with an unidentified component of the Rev nucleocytoplasmic transport complex. RESULTS To seek a possible mechanism that could explain how Nullbasic inhibits Rev activity, we used a proteomics approach to identify host cellular proteins that interact with Nullbasic. Forty-six Nullbasic-binding proteins were identified by mass spectrometry including the DEAD-box RNA helicase, DDX1. To determine the effect of DDX1 on Nullbasic-mediated Rev activity, we performed cell-based immunoprecipitation assays, Rev reporter assays and bio-layer interferometry (BLI) assays. Interaction between DDX1 and Nullbasic was observed by co-immunoprecipitation of Nullbasic with endogenous DDX1 from cell lysates. BLI assays showed a direct interaction between Nullbasic and DDX1. Nullbasic affected DDX1 subcellular distribution in a Rev-independent manner. Interestingly overexpression of DDX1 in cells not only restored Rev-dependent mRNA export and gene expression in a Rev reporter assay but also partly reversed Nullbasic-induced Rev subcellular mislocalization. Moreover, HIV-1 wild type Tat co-immunoprecipitated with DDX1 and overexpression of Tat could rescue the unspliced viral mRNA levels inhibited by Nullbasic in HIV-1 expressing cells. CONCLUSIONS Nullbasic was used to further define the complex mechanisms involved in the Rev-dependent nuclear export of the 9 kb and 4 kb viral RNAs. All together, these data indicate that DDX1 can be sequestered by Nullbasic leading to destabilization of the Rev nucleocytoplasmic transport complex and decreased levels of Rev-dependent viral transcripts. The outcomes support a role for DDX1 in maintenance of a Rev nuclear complex that transports viral RRE-containing mRNA to the cytoplasm. To our knowledge Nullbasic is the first anti-HIV protein that specifically targets the cellular protein DDX1 to block Rev's activity. Furthermore, our research raises the possibility that wild type Tat may play a previously unrecognized but very important role in Rev function.
Collapse
Affiliation(s)
- Min-Hsuan Lin
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia.
| | - Haran Sivakumaran
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia.
| | - Alun Jones
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia.
| | - Dongsheng Li
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia.
| | - Callista Harper
- Queensland Brain Institute, The University of Queensland, St. Lucia, Queensland, Australia.
| | - Ting Wei
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia.
| | - Hongping Jin
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia.
| | - Lina Rustanti
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia.
| | - Frederic A Meunier
- Australian Infectious Disease Research Centre, The University of Queensland, St. Lucia, Queensland, Australia. .,Queensland Brain Institute, The University of Queensland, St. Lucia, Queensland, Australia.
| | - Kirsten Spann
- Australian Infectious Disease Research Centre, The University of Queensland, St. Lucia, Queensland, Australia. .,School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland, Australia.
| | - David Harrich
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia. .,Australian Infectious Disease Research Centre, The University of Queensland, St. Lucia, Queensland, Australia.
| |
Collapse
|
135
|
Jayaraman B, Crosby DC, Homer C, Ribeiro I, Mavor D, Frankel AD. RNA-directed remodeling of the HIV-1 protein Rev orchestrates assembly of the Rev-Rev response element complex. eLife 2014; 3:e04120. [PMID: 25486594 PMCID: PMC4360532 DOI: 10.7554/elife.04120] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 12/06/2014] [Indexed: 12/27/2022] Open
Abstract
The HIV-1 protein Rev controls a critical step in viral replication by mediating the nuclear export of unspliced and singly-spliced viral mRNAs. Multiple Rev subunits assemble on the Rev Response Element (RRE), a structured region present in these RNAs, and direct their export through the Crm1 pathway. Rev-RRE assembly occurs via several Rev oligomerization and RNA-binding steps, but how these steps are coordinated to form an export-competent complex is unclear. Here, we report the first crystal structure of a Rev dimer-RRE complex, revealing a dramatic rearrangement of the Rev-dimer upon RRE binding through re-packing of its hydrophobic protein-protein interface. Rev-RNA recognition relies on sequence-specific contacts at the well-characterized IIB site and local RNA architecture at the second site. The structure supports a model in which the RRE utilizes the inherent plasticity of Rev subunit interfaces to guide the formation of a functional complex.
Collapse
MESH Headings
- Active Transport, Cell Nucleus
- Binding Sites
- Cell Line, Tumor
- Cell Nucleus/metabolism
- Cell Nucleus/virology
- Crystallography, X-Ray
- Cytosol/metabolism
- Cytosol/virology
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression Regulation
- HEK293 Cells
- HIV-1/genetics
- HIV-1/metabolism
- HeLa Cells
- Host-Pathogen Interactions
- Humans
- Karyopherins/genetics
- Karyopherins/metabolism
- Models, Molecular
- Protein Binding
- RNA Splicing
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Receptors, Cytoplasmic and Nuclear/genetics
- Receptors, Cytoplasmic and Nuclear/metabolism
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Response Elements
- Signal Transduction
- T-Lymphocytes/metabolism
- T-Lymphocytes/virology
- Virus Replication/genetics
- rev Gene Products, Human Immunodeficiency Virus/chemistry
- rev Gene Products, Human Immunodeficiency Virus/genetics
- rev Gene Products, Human Immunodeficiency Virus/metabolism
- Exportin 1 Protein
Collapse
Affiliation(s)
- Bhargavi Jayaraman
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - David C Crosby
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Christina Homer
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Isabel Ribeiro
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - David Mavor
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Alan D Frankel
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| |
Collapse
|
136
|
Ariumi Y. Multiple functions of DDX3 RNA helicase in gene regulation, tumorigenesis, and viral infection. Front Genet 2014; 5:423. [PMID: 25538732 PMCID: PMC4257086 DOI: 10.3389/fgene.2014.00423] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 11/19/2014] [Indexed: 12/11/2022] Open
Abstract
The DEAD-box RNA helicase DDX3 is a multifunctional protein involved in all aspects of RNA metabolism, including transcription, splicing, mRNA nuclear export, translation, RNA decay and ribosome biogenesis. In addition, DDX3 is also implicated in cell cycle regulation, apoptosis, Wnt-β-catenin signaling, tumorigenesis, and viral infection. Notably, recent studies suggest that DDX3 is a component of anti-viral innate immune signaling pathways. Indeed, DDX3 contributes to enhance the induction of anti-viral mediators, interferon (IFN) regulatory factor 3 and type I IFN. However, DDX3 seems to be an important target for several viruses, such as human immunodeficiency virus type 1 (HIV-1), hepatitis C virus (HCV), hepatitis B virus (HBV), and poxvirus. DDX3 interacts with HIV-1 Rev or HCV Core protein and modulates its function. At least, DDX3 is required for both HIV-1 and HCV replication. Therefore, DDX3 could be a novel therapeutic target for the development of drug against HIV-1 and HCV.
Collapse
Affiliation(s)
- Yasuo Ariumi
- Ariumi Project Laboratory, Center for AIDS Research - International Research Center for Medical Sciences, Kumamoto University Kumamoto, Japan
| |
Collapse
|
137
|
Aligeti M, Behrens RT, Pocock GM, Schindelin J, Dietz C, Eliceiri KW, Swanson CM, Malim MH, Ahlquist P, Sherer NM. Cooperativity among Rev-associated nuclear export signals regulates HIV-1 gene expression and is a determinant of virus species tropism. J Virol 2014; 88:14207-21. [PMID: 25275125 PMCID: PMC4249125 DOI: 10.1128/jvi.01897-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 09/23/2014] [Indexed: 01/20/2023] Open
Abstract
UNLABELLED Murine cells exhibit a profound block to HIV-1 virion production that was recently mapped to a species-specific structural attribute of the murine version of the chromosomal region maintenance 1 (mCRM1) nuclear export receptor and rescued by the expression of human CRM1 (hCRM1). In human cells, the HIV-1 Rev protein recruits hCRM1 to intron-containing viral mRNAs encoding the Rev response element (RRE), thereby facilitating viral late gene expression. Here we exploited murine 3T3 fibroblasts as a gain-of-function system to study hCRM1's species-specific role in regulating Rev's effector functions. We show that Rev is rapidly exported from the nucleus by mCRM1 despite only weak contributions to HIV-1's posttranscriptional stages. Indeed, Rev preferentially accumulates in the cytoplasm of murine 3T3 cells with or without hCRM1 expression, in contrast to human HeLa cells, where Rev exhibits striking en masse transitions between the nuclear and cytoplasmic compartments. Efforts to bias Rev's trafficking either into or out of the nucleus revealed that Rev encoding a second CRM1 binding domain (Rev-2xNES) or Rev-dependent viral gag-pol mRNAs bearing tandem RREs (GP-2xRRE), rescue virus particle production in murine cells even in the absence of hCRM1. Combined, these results suggest a model wherein Rev-associated nuclear export signals cooperate to regulate the number or quality of CRM1's interactions with viral Rev/RRE ribonucleoprotein complexes in the nucleus. This mechanism regulates CRM1-dependent viral gene expression and is a determinant of HIV-1's capacity to produce virions in nonhuman cell types. IMPORTANCE Cells derived from mice and other nonhuman species exhibit profound blocks to HIV-1 replication. Here we elucidate a block to HIV-1 gene expression attributable to the murine version of the CRM1 (mCRM1) nuclear export receptor. In human cells, hCRM1 regulates the nuclear export of viral intron-containing mRNAs through the activity of the viral Rev adapter protein that forms a multimeric complex on these mRNAs prior to recruiting hCRM1. We demonstrate that Rev-dependent gene expression is poor in murine cells despite the finding that, surprisingly, the bulk of Rev interacts efficiently with mCRM1 and is rapidly exported from the nucleus. Instead, we map the mCRM1 defect to the apparent inability of this factor to engage Rev multimers in the context of large viral Rev/RNA ribonucleoprotein complexes. These findings shed new light on HIV-1 gene regulation and could inform the development of novel antiviral strategies that target viral gene expression.
Collapse
Affiliation(s)
- Mounavya Aligeti
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ryan T Behrens
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ginger M Pocock
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA Morgridge Institute for Research, Madison, Wisconsin, USA
| | - Johannes Schindelin
- Morgridge Institute for Research, Madison, Wisconsin, USA Laboratory for Optical and Computational Instrumentation, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Christian Dietz
- Department of Computer and Information Science, University of Constance, Constance, Germany
| | - Kevin W Eliceiri
- Morgridge Institute for Research, Madison, Wisconsin, USA Laboratory for Optical and Computational Instrumentation, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Chad M Swanson
- Department of Infectious Diseases, King's College London, London, United Kingdom
| | - Michael H Malim
- Department of Infectious Diseases, King's College London, London, United Kingdom
| | - Paul Ahlquist
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA Morgridge Institute for Research, Madison, Wisconsin, USA Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nathan M Sherer
- McArdle Laboratory for Cancer Research and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| |
Collapse
|
138
|
Boons E, Li G, Vanstreels E, Vercruysse T, Pannecouque C, Vandamme AM, Daelemans D. A stably expressed llama single-domain intrabody targeting Rev displays broad-spectrum anti-HIV activity. Antiviral Res 2014; 112:91-102. [DOI: 10.1016/j.antiviral.2014.10.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 10/10/2014] [Accepted: 10/15/2014] [Indexed: 01/24/2023]
|
139
|
Levin A, Hayouka Z, Friedler A, Loyter A. Nucleocytoplasmic shuttling of HIV-1 integrase is controlled by the viral Rev protein. Nucleus 2014. [DOI: 10.4161/nucl.11300] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
|
140
|
Jeong WJ, Lim YB. Macrocyclic Peptides Self-Assemble into Robust Vesicles with Molecular Recognition Capabilities. Bioconjug Chem 2014; 25:1996-2003. [DOI: 10.1021/bc500367z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Woo-jin Jeong
- Translational Research Center for Protein Function Control and Department of Materials Science & Engineering, Yonsei University, Seoul 120-749, Korea
| | - Yong-beom Lim
- Translational Research Center for Protein Function Control and Department of Materials Science & Engineering, Yonsei University, Seoul 120-749, Korea
| |
Collapse
|
141
|
|
142
|
Perwitasari O, Johnson S, Yan X, Howerth E, Shacham S, Landesman Y, Baloglu E, McCauley D, Tamir S, Tompkins SM, Tripp RA. Verdinexor, a novel selective inhibitor of nuclear export, reduces influenza a virus replication in vitro and in vivo. J Virol 2014; 88:10228-43. [PMID: 24965445 PMCID: PMC4136318 DOI: 10.1128/jvi.01774-14] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 06/18/2014] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Influenza is a global health concern, causing death, morbidity, and economic losses. Chemotherapeutics that target influenza virus are available; however, rapid emergence of drug-resistant strains is common. Therapeutic targeting of host proteins hijacked by influenza virus to facilitate replication is an antiviral strategy to reduce the development of drug resistance. Nuclear export of influenza virus ribonucleoprotein (vRNP) from infected cells has been shown to be mediated by exportin 1 (XPO1) interaction with viral nuclear export protein tethered to vRNP. RNA interference screening has identified XPO1 as a host proinfluenza factor where XPO1 silencing results in reduced influenza virus replication. The Streptomyces metabolite XPO1 inhibitor leptomycin B (LMB) has been shown to limit influenza virus replication in vitro; however, LMB is toxic in vivo, which makes it unsuitable for therapeutic use. In this study, we tested the anti-influenza virus activity of a new class of orally available small-molecule selective inhibitors of nuclear export, specifically, the XPO1 antagonist KPT-335 (verdinexor). Verdinexor was shown to potently and selectively inhibit vRNP export and effectively inhibited the replication of various influenza virus A and B strains in vitro, including pandemic H1N1 virus, highly pathogenic H5N1 avian influenza virus, and the recently emerged H7N9 strain. In vivo, prophylactic and therapeutic administration of verdinexor protected mice against disease pathology following a challenge with influenza virus A/California/04/09 or A/Philippines/2/82-X79, as well as reduced lung viral loads and proinflammatory cytokine expression, while having minimal toxicity. These studies show that verdinexor acts as a novel anti-influenza virus therapeutic agent. IMPORTANCE Antiviral drugs represent important means of influenza virus control. However, substantial resistance to currently approved influenza therapeutic drugs has developed. New antiviral approaches are required to address drug resistance and reduce the burden of influenza virus-related disease. This study addressed critical preclinical studies for the development of verdinexor (KPT-335) as a novel antiviral drug. Verdinexor blocks progeny influenza virus genome nuclear export, thus effectively inhibiting virus replication. Verdinexor was found to limit the replication of various strains of influenza A and B viruses, including a pandemic H1N1 influenza virus strain, a highly pathogenic H5N1 avian influenza virus strain, and a recently emerging H7N9 influenza virus strain. Importantly, oral verdinexor treatments, given prophylactically or therapeutically, were efficacious in limiting lung virus burdens in influenza virus-infected mice, in addition to limiting lung proinflammatory cytokine expression, pathology, and death. Thus, this study demonstrated that verdinexor is efficacious against influenza virus infection in vitro and in vivo.
Collapse
Affiliation(s)
- Olivia Perwitasari
- Department of Infectious Diseases, University of Georgia College of Veterinary Medicine, Athens, Georgia, USA
| | - Scott Johnson
- Department of Infectious Diseases, University of Georgia College of Veterinary Medicine, Athens, Georgia, USA
| | - Xiuzhen Yan
- Department of Infectious Diseases, University of Georgia College of Veterinary Medicine, Athens, Georgia, USA
| | - Elizabeth Howerth
- Department of Pathology, University of Georgia College of Veterinary Medicine, Athens, Georgia, USA
| | - Sharon Shacham
- Karyopharm Therapeutics, Inc., Natick, Massachusetts, USA
| | | | - Erkan Baloglu
- Karyopharm Therapeutics, Inc., Natick, Massachusetts, USA
| | | | - Sharon Tamir
- Karyopharm Therapeutics, Inc., Natick, Massachusetts, USA
| | - S Mark Tompkins
- Department of Infectious Diseases, University of Georgia College of Veterinary Medicine, Athens, Georgia, USA
| | - Ralph A Tripp
- Department of Infectious Diseases, University of Georgia College of Veterinary Medicine, Athens, Georgia, USA
| |
Collapse
|
143
|
Cunyat F, Beerens N, García E, Clotet B, Kjems J, Cabrera C. Functional analyses reveal extensive RRE plasticity in primary HIV-1 sequences selected under selective pressure. PLoS One 2014; 9:e106299. [PMID: 25170621 PMCID: PMC4149556 DOI: 10.1371/journal.pone.0106299] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 08/05/2014] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND HIV-1 Rev response element (RRE) is a functional region of viral RNA lying immediately downstream to the junction of gp120 and gp41 in the env coding sequence. The RRE is essential for HIV replication and binds with the Rev protein to facilitate the export of viral mRNA from nucleus to cytoplasm. It has been suggested that changes in the predicted secondary structure of primary RRE sequences impact the function of the RREs; however, functional assays have not yet been performed. The aim of this study was to characterize the genetic, structural and functional variation in the RRE primary sequences selected in vivo by Enfuvirtide pressure. RESULTS Multiple RRE variants were obtained from viruses isolated from patients who failed an Enfuvirtide-containing regimen. Different alterations were observed in the predicted RRE secondary structures, with the abrogation of the primary Rev binding site in one of the variants. In spite of this, most of the RRE variants were able to bind Rev and promote the cytoplasmic export of the viral mRNAs with equivalent efficiency in a cell-based assay. Only RRE45 and RRE40-45 showed an impaired ability to bind Rev in a gel-shift binding assay. Unexpectedly, this impairment was not reflected in functional capacity when RNA export was evaluated using a reporter assay, or during virus replication in lymphoid cells, suggesting that in vivo the RRE would be highly malleable. CONCLUSIONS The Rev-RRE functionality is unaffected in RRE variants selected in patients failing an ENF-containing regimen. Our data show that the current understanding of the Rev-RRE complex structure does not suffice and fails to rationally predict the function of naturally occurring RRE mutants. Therefore, this data should be taken into account in the development of antiviral agents that target the RRE-Rev complex.
Collapse
Affiliation(s)
- Francesc Cunyat
- IrsiCaixa-HIVACAT, Institut de Recerca en Ciències de la Salut Germans Trias i Pujol (IGTP), Hospital Germans Trias, Universitat Autònoma de Barcelona, Badalona, Barcelona, Catalonia, Spain
| | - Nancy Beerens
- Department of Molecular Biology, Aarhus University, Aarhus, Denmark
| | - Elisabet García
- IrsiCaixa-HIVACAT, Institut de Recerca en Ciències de la Salut Germans Trias i Pujol (IGTP), Hospital Germans Trias, Universitat Autònoma de Barcelona, Badalona, Barcelona, Catalonia, Spain
| | - Bonaventura Clotet
- IrsiCaixa-HIVACAT, Institut de Recerca en Ciències de la Salut Germans Trias i Pujol (IGTP), Hospital Germans Trias, Universitat Autònoma de Barcelona, Badalona, Barcelona, Catalonia, Spain
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center (iNANO), Molecular Biology and Genetics Department, Aarhus University, Aarhus, Denmark
| | - Cecilia Cabrera
- IrsiCaixa-HIVACAT, Institut de Recerca en Ciències de la Salut Germans Trias i Pujol (IGTP), Hospital Germans Trias, Universitat Autònoma de Barcelona, Badalona, Barcelona, Catalonia, Spain
| |
Collapse
|
144
|
Bai Y, Tambe A, Zhou K, Doudna JA. RNA-guided assembly of Rev-RRE nuclear export complexes. eLife 2014; 3:e03656. [PMID: 25163983 PMCID: PMC4142337 DOI: 10.7554/elife.03656] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 08/05/2014] [Indexed: 11/13/2022] Open
Abstract
HIV replication requires nuclear export of unspliced and singly spliced viral transcripts. Although a unique RNA structure has been proposed for the Rev-response element (RRE) responsible for viral mRNA export, how it recruits multiple HIV Rev proteins to form an export complex has been unclear. We show here that initial binding of Rev to the RRE triggers RNA tertiary structural changes, enabling further Rev binding and the rapid formation of a viral export complex. Analysis of the Rev-RRE assembly pathway using SHAPE-Seq and small-angle X-ray scattering (SAXS) reveals two major steps of Rev-RRE complex formation, beginning with rapid Rev binding to a pre-organized region presenting multiple Rev binding sites. This step induces long-range remodeling of the RNA to expose a cryptic Rev binding site, enabling rapid assembly of additional Rev proteins into the RNA export complex. This kinetic pathway may help maintain the balance between viral replication and maturation.DOI: http://dx.doi.org/10.7554/eLife.03656.001.
Collapse
Affiliation(s)
- Yun Bai
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Akshay Tambe
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Kaihong Zhou
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States Department of Chemistry, University of California, Berkeley, Berkeley, United States Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| |
Collapse
|
145
|
Bera A, Perkins EM, Zhu J, Zhu H, Desai P. DNA binding and condensation properties of the herpes simplex virus type 1 triplex protein VP19C. PLoS One 2014; 9:e104640. [PMID: 25121591 PMCID: PMC4133253 DOI: 10.1371/journal.pone.0104640] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 07/10/2014] [Indexed: 12/02/2022] Open
Abstract
Herpesvirus capsids are regular icosahedrons with a diameter of a 125 nm and are made up of 162 capsomeres arranged on a T = 16 lattice. The capsomeres (VP5) interact with the triplex structure, which is a unique structural feature of herpesvirus capsid shells. The triplex is a heterotrimeric complex; one molecule of VP19C and two of VP23 form a three-pronged structure that acts to stabilize the capsid shell through interactions with adjacent capsomeres. VP19C interacts with VP23 and with the major capsid protein VP5 and is required for the nuclear localization of VP23. Mutation of VP19C results in the abrogation of capsid shell synthesis. Analysis of the sequence of VP19C showed the N-terminus of VP19C is very basic and glycine rich. It was hypothesized that this domain could potentially bind to DNA. In this study an electrophoretic mobility shift assay (EMSA) and a DNA condensation assay were performed to demonstrate that VP19C can bind DNA. Purified VP19C was able to bind to both a DNA fragment of HSV-1 origin as well as a bacterial plasmid sequence indicating that this activity is non-specific. Ultra-structural imaging of the nucleo-protein complexes revealed that VP19C condensed the DNA and forms toroidal DNA structures. Both the DNA binding and condensing properties of VP19C were mapped to the N-terminal 72 amino acids of the protein. Mutational studies revealed that the positively charged arginine residues in this N-terminal domain are required for this binding. This DNA binding activity, which resides in a non-conserved region of the protein could be required for stabilization of HSV-1 DNA association in the capsid shell.
Collapse
Affiliation(s)
- Alakesh Bera
- Viral Oncology Program, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail:
| | - Edward M. Perkins
- Department of Biology and Integrated Imaging Center, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Jian Zhu
- HiT Center and Department of Pharmacology and Molecular Sciences, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Heng Zhu
- HiT Center and Department of Pharmacology and Molecular Sciences, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Prashant Desai
- Viral Oncology Program, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Johns Hopkins University, Baltimore, Maryland, United States of America
| |
Collapse
|
146
|
Zhabokritsky A, Mansouri S, Hudak KA. Pokeweed antiviral protein alters splicing of HIV-1 RNAs, resulting in reduced virus production. RNA (NEW YORK, N.Y.) 2014; 20:1238-1247. [PMID: 24951553 PMCID: PMC4105749 DOI: 10.1261/rna.043141.113] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 05/06/2014] [Indexed: 06/03/2023]
Abstract
Processing of HIV-1 transcripts results in three populations in the cytoplasm of infected cells: full-length RNA, singly spliced, and multiply spliced RNAs. Rev, regulator of virion expression, is an essential regulatory protein of HIV-1 required for transporting unspliced and singly spliced viral transcripts from the nucleus to the cytoplasm. Export allows these RNAs to be translated and the full-length RNA to be packaged into virus particles. In our study, we investigate the activity of pokeweed antiviral protein (PAP), a glycosidase isolated from the pokeweed plant Phytolacca americana, on the processing of viral RNAs. We show that coexpression of PAP with a proviral clone alters the splicing ratio of HIV-1 RNAs. Specifically, PAP causes the accumulation of multiply spliced 2-kb RNAs at the expense of full-length 9-kb and singly spliced 4-kb RNAs. The change in splicing ratio is due to a decrease in activity of Rev. We show that PAP depurinates the rev open reading frame and that this damage to the viral RNA inhibits its translation. By decreasing Rev expression, PAP indirectly reduces the availability of full-length 9-kb RNA for packaging and translation of the encoded structural proteins required for synthesis of viral particles. The decline we observe in virus protein expression is not due to cellular toxicity as PAP did not diminish translation rate. Our results describing the reduced activity of a regulatory protein of HIV-1, with resulting change in virus mRNA ratios, provides new insight into the antiviral mechanism of PAP.
Collapse
Affiliation(s)
- Alice Zhabokritsky
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada
| | - Sheila Mansouri
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada
| | - Katalin A Hudak
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada
| |
Collapse
|
147
|
Burugu S, Daher A, Meurs EF, Gatignol A. HIV-1 translation and its regulation by cellular factors PKR and PACT. Virus Res 2014; 193:65-77. [PMID: 25064266 DOI: 10.1016/j.virusres.2014.07.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 07/13/2014] [Accepted: 07/14/2014] [Indexed: 12/24/2022]
Abstract
The synthesis of proteins from viral mRNA is the first step towards viral assembly. Viruses are dependent upon the cellular translation machinery to synthesize their own proteins. The synthesis of proteins from the human immunodeficiency virus (HIV) type 1 and 2 RNAs utilize several alternative mechanisms. The regulation of viral protein production requires a constant interplay between viral requirements and the cell response to viral infection. Among the antiviral cell responses, the interferon-induced RNA activated protein kinase, PKR, regulates the cellular and viral translation. During HIV-1 infection, PKR activation is highly regulated by viral and cellular factors. The cellular TAR RNA Binding Protein, TRBP, the Adenosine Deaminase acting on RNA, ADAR1, and the PKR Activator, PACT, play important roles. Recent data show that PACT changes its function from activator to inhibitor in HIV-1 infected cells. Therefore, HIV-1 has evolved to replicate in cells in which TRBP, ADAR1 and PACT prevent PKR activation to allow efficient viral protein synthesis. This proper translation will initiate the assembly of viral particles.
Collapse
Affiliation(s)
- Samantha Burugu
- Virus-cell Interactions Laboratory, Lady Davis Institute for Medical Research, Montréal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
| | - Aïcha Daher
- Virus-cell Interactions Laboratory, Lady Davis Institute for Medical Research, Montréal, QC, Canada
| | - Eliane F Meurs
- Institut Pasteur, Department of Virology, Hepacivirus and Innate Immunity Unit, Paris, France
| | - Anne Gatignol
- Virus-cell Interactions Laboratory, Lady Davis Institute for Medical Research, Montréal, QC, Canada; Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada; Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, Canada.
| |
Collapse
|
148
|
Han SH, Kim HW, Jeong WJ, Lim YB. Macromolecular sensing of RNAs by exploiting conformational changes in supramolecular nanostructures. Biomacromolecules 2014; 15:2642-7. [PMID: 24855025 DOI: 10.1021/bm500480y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Here, we report on a ratiometric fluorescence biosensor based on self-assembled peptide nanostructures (SPN), which can respond to conformational changes induced by RNA ligand binding. The design of the SPN biosensor was inspired by the conformational stabilization and multimerization behaviors of the HIV-1 Rev protein induced by cooperative protein-protein and protein-RNA interactions. Because conformation-sensitive SPN biosensors can orchestrate binding and signal transduction events, they can be developed as highly sophisticated and smart nanomaterials for biosensing.
Collapse
Affiliation(s)
- So-hee Han
- Translational Research Center for Protein Function Control and Department of Materials Science and Engineering, Yonsei University , Seoul 120-749, Korea
| | | | | | | |
Collapse
|
149
|
Godinho RMDC, Matassoli FL, Lucas CGDO, Rigato PO, Gonçalves JLS, Sato MN, Maciel M, Peçanha LMT, August JT, Marques ETDA, de Arruda LB. Regulation of HIV-Gag expression and targeting to the endolysosomal/secretory pathway by the luminal domain of lysosomal-associated membrane protein (LAMP-1) enhance Gag-specific immune response. PLoS One 2014; 9:e99887. [PMID: 24932692 PMCID: PMC4059647 DOI: 10.1371/journal.pone.0099887] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 05/19/2014] [Indexed: 12/17/2022] Open
Abstract
We have previously demonstrated that a DNA vaccine encoding HIV-p55gag in association with the lysosomal associated membrane protein-1 (LAMP-1) elicited a greater Gag-specific immune response, in comparison to a DNA encoding the native gag. In vitro studies have also demonstrated that LAMP/Gag was highly expressed and was present in MHCII containing compartments in transfected cells. In this study, the mechanisms involved in these processes and the relative contributions of the increased expression and altered traffic for the enhanced immune response were addressed. Cells transfected with plasmid DNA constructs containing p55gag attached to truncated sequences of LAMP-1 showed that the increased expression of gag mRNA required p55gag in frame with at least 741 bp of the LAMP-1 luminal domain. LAMP luminal domain also showed to be essential for Gag traffic through lysosomes and, in this case, the whole sequence was required. Further analysis of the trafficking pathway of the intact LAMP/Gag chimera demonstrated that it was secreted, at least in part, associated with exosome-like vesicles. Immunization of mice with LAMP/gag chimeric plasmids demonstrated that high expression level alone can induce a substantial transient antibody response, but targeting of the antigen to the endolysosomal/secretory pathways was required for establishment of cellular and memory response. The intact LAMP/gag construct induced polyfunctional CD4+ T cell response, which presence at the time of immunization was required for CD8+ T cell priming. LAMP-mediated targeting to endolysosomal/secretory pathway is an important new mechanistic element in LAMP-mediated enhanced immunity with applications to the development of novel anti-HIV vaccines and to general vaccinology field.
Collapse
Affiliation(s)
- Rodrigo Maciel da Costa Godinho
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Flavio Lemos Matassoli
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Paula Ordonhez Rigato
- Laboratorio de Dermatologia e Imunodeficiencias, LIM-56, Departamento de Dermatologia, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Jorge Luiz Santos Gonçalves
- Departamento de Imunologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Maria Notomi Sato
- Laboratorio de Dermatologia e Imunodeficiencias, LIM-56, Departamento de Dermatologia, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Milton Maciel
- Enteric Diseases Department, Infectious Diseases Directorate, Naval Medical Research Center, Silver Spring, Maryland, United States of America; Department of Pharmacology and Molecular Sciences, The Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Ligia Maria Torres Peçanha
- Departamento de Imunologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - J Thomas August
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Ernesto Torres de Azevedo Marques
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America; Department of Infectious Diseases and Microbiology, Center for Vaccine Research, Pittsburgh, Pennsylvania, United States of America; Departamento de Virologia, Fiocruz - Pernambuco, Recife, Brazil
| | - Luciana Barros de Arruda
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| |
Collapse
|
150
|
Taniguchi I, Mabuchi N, Ohno M. HIV-1 Rev protein specifies the viral RNA export pathway by suppressing TAP/NXF1 recruitment. Nucleic Acids Res 2014; 42:6645-58. [PMID: 24753416 PMCID: PMC4041468 DOI: 10.1093/nar/gku304] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 03/31/2014] [Accepted: 03/31/2014] [Indexed: 01/11/2023] Open
Abstract
Nuclear RNA export pathways in eukaryotes are often linked to the fate of a given RNA. Therefore, the choice of export pathway should be well-controlled to avoid an unfavorable effect on gene expression. Although some RNAs could be exported by more than one pathway, little is known about how the choice is regulated. This issue is highlighted when the human immunodeficiency virus type 1 (HIV-1) Rev protein induces the export of singly spliced and unspliced HIV-1 transcripts. How these RNAs are exported is not well understood because such transcripts should have the possibility of utilizing CRM1-dependent export via Rev or cellular TAP/NXF1-dependent export via the transcription/export (TREX) complex, or both. Here we found that Rev suppressed TAP/NXF1-dependent export of model RNA substrates that recapitulated viral transcripts. In this effect, Rev interacted with the cap-binding complex and inhibited the recruitment of the TREX complex. Thus, Rev controls the identity of the factor occupying the cap-proximal region that determines the RNA export pathway. This ribonucleoprotein remodeling activity of Rev may favor viral gene expression.
Collapse
Affiliation(s)
- Ichiro Taniguchi
- Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan
| | - Naoto Mabuchi
- Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan
| | - Mutsuhito Ohno
- Institute for Virus Research, Kyoto University, Kyoto 606-8507, Japan
| |
Collapse
|