1
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Tipo J, Gottipati K, Slaton M, Gonzalez-Gutierrez G, Choi KH. Structure of HIV-1 RRE stem-loop II identifies two conformational states of the high-affinity Rev binding site. Nat Commun 2024; 15:4198. [PMID: 38760344 PMCID: PMC11101469 DOI: 10.1038/s41467-024-48162-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 04/22/2024] [Indexed: 05/19/2024] Open
Abstract
During HIV infection, specific RNA-protein interaction between the Rev response element (RRE) and viral Rev protein is required for nuclear export of intron-containing viral mRNA transcripts. Rev initially binds the high-affinity site in stem-loop II, which promotes oligomerization of additional Rev proteins on RRE. Here, we present the crystal structure of RRE stem-loop II in distinct closed and open conformations. The high-affinity Rev-binding site is located within the three-way junction rather than the predicted stem IIB. The closed and open conformers differ in their non-canonical interactions within the three-way junction, and only the open conformation has the widened major groove conducive to initial Rev interaction. Rev binding assays show that RRE stem-loop II has high- and low-affinity binding sites, each of which binds a Rev dimer. We propose a binding model, wherein Rev-binding sites on RRE are sequentially created through structural rearrangements induced by Rev-RRE interactions.
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Affiliation(s)
- Jerricho Tipo
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, TX, 77555, USA
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Keerthi Gottipati
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47405, USA
| | - Michael Slaton
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47405, USA
| | | | - Kyung H Choi
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch, Galveston, TX, 77555, USA.
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, 47405, USA.
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology, The University of Texas Medical Branch, Galveston, TX, 77555, USA.
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2
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Payá G, Bautista V, Pastor-Soler S, Camacho M, Esclapez J, Bonete MJ. Analysis of Lsm Protein-Mediated Regulation in the Haloarchaeon Haloferax mediterranei. Int J Mol Sci 2024; 25:580. [PMID: 38203750 PMCID: PMC10779274 DOI: 10.3390/ijms25010580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 12/20/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
The Sm protein superfamily includes Sm, like-Sm (Lsm), and Hfq found in the Eukarya, Archaea, and Bacteria domains. Archaeal Lsm proteins have been shown to bind sRNAs and are probably involved in various cellular processes, suggesting a similar function in regulating sRNAs by Hfq in bacteria. Moreover, archaeal Lsm proteins probably represent the ancestral Lsm domain from which eukaryotic Sm proteins have evolved. In this work, Haloferax mediterranei was used as a model organism because it has been widely used to investigate the nitrogen cycle and its regulation in Haloarchaea. Predicting this protein's secondary and tertiary structures has resulted in a three-dimensional model like the solved Lsm protein structure of Archaeoglobus fulgidus. To obtain information on the oligomerization state of the protein, homologous overexpression and purification by means of molecular exclusion chromatography have been performed. The results show that this protein can form hexameric complexes, which can aggregate into 6 or 12 hexameric rings depending on the NaCl concentration and without RNA. In addition, the study of transcriptional expression via microarrays has allowed us to obtain the target genes regulated by the Lsm protein under nutritional stress conditions: nitrogen or carbon starvation. Microarray analysis has shown the first universal stress proteins (USP) in this microorganism that mediate survival in situations of nitrogen deficiency.
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Affiliation(s)
| | | | | | | | | | - María-José Bonete
- Department of Biochemistry and Molecular Biology and Soil Science and Agricultural Chemistry, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain; (G.P.); (V.B.); (S.P.-S.); (M.C.); (J.E.)
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3
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Dzhivhuho G, Holsey J, Honeycutt E, O'Farrell H, Rekosh D, Hammarskjold ML, Jackson PEH. HIV-1 Rev-RRE functional activity in primary isolates is highly dependent on minimal context-dependent changes in Rev. Sci Rep 2022; 12:18416. [PMID: 36319640 PMCID: PMC9626594 DOI: 10.1038/s41598-022-21714-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/30/2022] [Indexed: 01/01/2023] Open
Abstract
During HIV infection, intron-containing viral mRNAs are exported from the cell nucleus to the cytoplasm to complete the replication cycle. Cellular restrictions on the export of incompletely spliced transcripts are overcome by a viral protein, Rev, and an RNA structure found in all unspliced and incompletely spliced viral mRNAs, the Rev Response Element (RRE). Primary HIV isolates display substantial variation in the sequence and functional activity of Rev proteins. We analyzed Rev from two primary isolates with disparate activity that resulted in differences in in vitro fitness of replication-competent viral constructs. The results showed that amino acid differences within the oligomerization domain, but not the arginine-rich motif or the nuclear export signal, determined the level of Rev activity. Two specific amino acid substitutions were sufficient to alter the low-activity Rev to a high-activity phenotype. Other mutations in Rev sequences had unpredictable effects on activity that differed between the two Rev backbones. The sensitivity of Rev function level to small sequence changes likely permits modulation of Rev-RRE activity during HIV infection, which may play a role in pathogenesis. The functional consequences of Rev mutations differed between primary isolates, highlighting the challenge of generalizing studies of Rev conducted using laboratory HIV strains.
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Affiliation(s)
- Godfrey Dzhivhuho
- Myles H. Thaler Center for HIV and Human Retrovirus Research, University of Virginia, Charlottesville, VA, USA
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Jordan Holsey
- Myles H. Thaler Center for HIV and Human Retrovirus Research, University of Virginia, Charlottesville, VA, USA
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Ethan Honeycutt
- Myles H. Thaler Center for HIV and Human Retrovirus Research, University of Virginia, Charlottesville, VA, USA
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Heather O'Farrell
- Myles H. Thaler Center for HIV and Human Retrovirus Research, University of Virginia, Charlottesville, VA, USA
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - David Rekosh
- Myles H. Thaler Center for HIV and Human Retrovirus Research, University of Virginia, Charlottesville, VA, USA
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Marie-Louise Hammarskjold
- Myles H. Thaler Center for HIV and Human Retrovirus Research, University of Virginia, Charlottesville, VA, USA
- Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Patrick E H Jackson
- Myles H. Thaler Center for HIV and Human Retrovirus Research, University of Virginia, Charlottesville, VA, USA.
- Division of Infectious Diseases and International Health, School of Medicine, University of Virginia, Charlottesville, VA, USA.
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4
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Spittler D, Indorato RL, Boeri Erba E, Delaforge E, Signor L, Harris SJ, Garcia-Saez I, Palencia A, Gabel F, Blackledge M, Noirclerc-Savoye M, Petosa C. Binding stoichiometry and structural model of the HIV-1 Rev/importin β complex. Life Sci Alliance 2022; 5:5/10/e202201431. [PMID: 35995566 PMCID: PMC9396022 DOI: 10.26508/lsa.202201431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 11/24/2022] Open
Abstract
HIV-1 Rev mediates the nuclear export of intron-containing viral RNA transcripts and is essential for viral replication. Rev is imported into the nucleus by the host protein importin β (Impβ), but how Rev associates with Impβ is poorly understood. Here, we report biochemical, mutational, and biophysical studies of the Impβ/Rev complex. We show that Impβ binds two Rev monomers through independent binding sites, in contrast to the 1:1 binding stoichiometry observed for most Impβ cargos. Peptide scanning data and charge-reversal mutations identify the N-terminal tip of Rev helix α2 within Rev's arginine-rich motif (ARM) as a primary Impβ-binding epitope. Cross-linking mass spectrometry and compensatory mutagenesis data combined with molecular docking simulations suggest a structural model in which one Rev monomer binds to the C-terminal half of Impβ with Rev helix α2 roughly parallel to the HEAT-repeat superhelical axis, whereas the other monomer binds to the N-terminal half. These findings shed light on the molecular basis of Rev recognition by Impβ and highlight an atypical binding behavior that distinguishes Rev from canonical cellular Impβ cargos.
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Affiliation(s)
- Didier Spittler
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Rose-Laure Indorato
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Elisabetta Boeri Erba
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Elise Delaforge
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Luca Signor
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Simon J Harris
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Isabel Garcia-Saez
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Andrés Palencia
- Institute for Advanced Biosciences, Structural Biology of Novel Targets in Human Diseases, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Grenoble, France
| | - Frank Gabel
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Martin Blackledge
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Marjolaine Noirclerc-Savoye
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
| | - Carlo Petosa
- Université Grenoble Alpes, Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale, Grenoble, France
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5
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Hansen T, Baris J, Zhao M, Sutton RE. Cell-based and cell-free firefly luciferase complementation assay to quantify Human Immunodeficiency Virus type 1 Rev-Rev interaction. Virology 2022; 576:30-41. [DOI: 10.1016/j.virol.2022.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 08/17/2022] [Accepted: 08/20/2022] [Indexed: 11/17/2022]
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6
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Kim DI, Han SH, Park H, Choi S, Kaur M, Hwang E, Han SJ, Ryu JY, Cheong HK, Barnwal RP, Lim YB. Pseudo-Isolated α-Helix Platform for the Recognition of Deep and Narrow Targets. J Am Chem Soc 2022; 144:15519-15528. [PMID: 35972994 DOI: 10.1021/jacs.2c03858] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although interest in stabilized α-helical peptides as next-generation therapeutics for modulating biomolecular interfaces is increasing, peptides have limited functionality and stability due to their small size. In comparison, α-helical ligands based on proteins can make steric clash with targets due to their large size. Here, we report the design of a monomeric pseudo-isolated α-helix (mPIH) system in which proteins behave as if they are peptides. The designed proteins contain α-helix ligands that do not require any covalent chemical modification, do not have frayed ends, and importantly can make sterically favorable interactions similar to isolated peptides. An optimal mPIH showed a more than 100-fold increase in target selectivity, which might be related to the advantages in conformational selection due to the absence of frayed ends. The α-helical ligand in the mPIH displayed high thermal stability well above human body temperature and showed reversible and rapid folding/unfolding transitions. Thus, mPIH can become a promising protein-based platform for developing stabilized α-helix pharmaceuticals.
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Affiliation(s)
- Dong-In Kim
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - So-Hee Han
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Hahnbeom Park
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Sehwan Choi
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Mandeep Kaur
- Department of Biophysics, Panjab University, Chandigarh 160014, India
| | - Euimin Hwang
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Seong-Jae Han
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Jung-Yeon Ryu
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Hae-Kap Cheong
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang 28119, Republic of Korea
| | | | - Yong-Beom Lim
- Department of Materials Science and Engineering, Yonsei University, Seoul 03722, Republic of Korea
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7
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Hanson HM, Willkomm NA, Yang H, Mansky LM. Human Retrovirus Genomic RNA Packaging. Viruses 2022; 14:1094. [PMID: 35632835 PMCID: PMC9142903 DOI: 10.3390/v14051094] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/12/2022] [Accepted: 05/14/2022] [Indexed: 02/07/2023] Open
Abstract
Two non-covalently linked copies of the retrovirus genome are specifically recruited to the site of virus particle assembly and packaged into released particles. Retroviral RNA packaging requires RNA export of the unspliced genomic RNA from the nucleus, translocation of the genome to virus assembly sites, and specific interaction with Gag, the main viral structural protein. While some aspects of the RNA packaging process are understood, many others remain poorly understood. In this review, we provide an update on recent advancements in understanding the mechanism of RNA packaging for retroviruses that cause disease in humans, i.e., HIV-1, HIV-2, and HTLV-1, as well as advances in the understanding of the details of genomic RNA nuclear export, genome translocation to virus assembly sites, and genomic RNA dimerization.
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Affiliation(s)
- Heather M. Hanson
- Molecular, Cellular, Developmental Biology, and Genetics Graduate Program, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA;
- Institute for Molecular Virology, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA; (N.A.W.); (H.Y.)
| | - Nora A. Willkomm
- Institute for Molecular Virology, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA; (N.A.W.); (H.Y.)
- DDS-PhD Dual Degree Program, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
| | - Huixin Yang
- Institute for Molecular Virology, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA; (N.A.W.); (H.Y.)
- Comparative Molecular Biosciences Graduate Program, University of Minnesota—Twin Cities, St. Paul, MN 55455, USA
| | - Louis M. Mansky
- Molecular, Cellular, Developmental Biology, and Genetics Graduate Program, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA;
- Institute for Molecular Virology, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA; (N.A.W.); (H.Y.)
- DDS-PhD Dual Degree Program, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
- Comparative Molecular Biosciences Graduate Program, University of Minnesota—Twin Cities, St. Paul, MN 55455, USA
- Masonic Cancer Center, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
- Division of Basic Sciences, School of Dentistry, University of Minnesota—Twin Cities, Minneapolis, MN 55455, USA
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8
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Jackson PEH, Dzhivhuho G, Rekosh D, Hammarskjold ML. Sequence and Functional Variation in the HIV-1 Rev Regulatory Axis. Curr HIV Res 2021; 18:85-98. [PMID: 31906839 DOI: 10.2174/1570162x18666200106112842] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/22/2019] [Accepted: 12/02/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND To complete its replication cycle, HIV-1 requires the nucleocytoplasmic export of intron-containing viral mRNAs. This process is ordinarily restricted by the cell, but HIV overcomes the block by means of a viral protein, Rev, and an RNA secondary structure found in all unspliced and incompletely spliced viral mRNAs called the Rev Response Element (RRE). In vivo activity of the Rev-RRE axis requires Rev binding to the RRE, oligomerization of Rev to form a competent ribonucleoprotein complex, and recruitment of cellular factors including Crm1 and RanGTP in order to export the targeted transcript. Sequence variability is observed among primary isolates in both Rev and the RRE, and the activity of both can be modulated through relatively small sequence changes. Primary isolates show differences in Rev-RRE activity and a few studies have found a correlation between lower Rev-RRE activity and slower progression of clinical disease. Lower Rev-RRE activity has also been associated with the evasion of cytotoxic T lymphocyte mediated killing. CONCLUSION The HIV-1 Rev-RRE regulatory axis is an understudied mechanism by which viral adaptation to diverse immune milieus may take place. There is evidence that this adaptation plays a role in HIV pathogenesis, particularly in immune evasion and latency, but further studies with larger sample sizes are warranted.
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Affiliation(s)
- Patrick E H Jackson
- Division of Infectious Diseases and International Health, School of Medicine, University of Virginia, Charlottesville, Virginia United States.,Myles H. Thaler Center for HIV and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia, United States
| | - Godfrey Dzhivhuho
- Myles H. Thaler Center for HIV and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia, United States.,Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, Virginia, United States
| | - David Rekosh
- Myles H. Thaler Center for HIV and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia, United States.,Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, Virginia, United States
| | - Marie-Louise Hammarskjold
- Myles H. Thaler Center for HIV and Human Retrovirus Research, University of Virginia, Charlottesville, Virginia, United States.,Department of Microbiology, Immunology, and Cancer Biology, School of Medicine, University of Virginia, Charlottesville, Virginia, United States
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9
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Sherpa C, Grice SFJL. Structural Fluidity of the Human Immunodeficiency Virus Rev Response Element. Viruses 2020; 12:v12010086. [PMID: 31940828 PMCID: PMC7019801 DOI: 10.3390/v12010086] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/07/2020] [Accepted: 01/09/2020] [Indexed: 01/22/2023] Open
Abstract
Nucleocytoplasmic transport of unspliced and partially spliced human immunodeficiency virus (HIV) RNA is mediated in part by the Rev response element (RRE), a ~350 nt cis-acting element located in the envelope coding region of the viral genome. Understanding the interaction of the RRE with the viral Rev protein, cellular co-factors, and its therapeutic potential has been the subject of almost three decades of structural studies, throughout which a recurring discussion theme has been RRE topology, i.e., whether it comprises 4 or 5 stem-loops (SLs) and whether this has biological significance. Moreover, while in vitro mutagenesis allows the construction of 4 SL and 5 SL RRE conformers and testing of their roles in cell culture, it has not been immediately clear if such findings can be translated to a clinical setting. Herein, we review several articles demonstrating remarkable flexibility of the HIV-1 and HIV-2 RREs following initial observations that HIV-1 resistance to trans-dominant Rev therapy was founded in structural rearrangement of its RRE. These observations can be extended not only to cell culture studies demonstrating a growth advantage for the 5 SL RRE conformer but also to evolution in RRE topology in patient isolates. Finally, RRE conformational flexibility provides a target for therapeutic intervention, and we describe high throughput screening approaches to exploit this property.
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10
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Evolution of the HIV-1 Rev Response Element during Natural Infection Reveals Nucleotide Changes That Correlate with Altered Structure and Increased Activity over Time. J Virol 2019; 93:JVI.02102-18. [PMID: 30867301 DOI: 10.1128/jvi.02102-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/05/2019] [Indexed: 12/15/2022] Open
Abstract
The HIV-1 Rev response element (RRE) is a cis-acting RNA element characterized by multiple stem-loops. Binding and multimerization of the HIV Rev protein on the RRE promote the nucleocytoplasmic export of incompletely spliced mRNAs, an essential step in HIV replication. Most of our understanding of the Rev-RRE regulatory axis comes from studies of lab-adapted HIV clones. However, in human infection, HIV evolves rapidly, and mechanistic studies of naturally occurring Rev and RRE sequences are essential to understanding this system. We previously described the functional activity of two RREs found in circulating viruses in a patient followed during the course of HIV infection. The early RRE was less functionally active than the late RRE, despite differing in sequence by only 4 nucleotides. In this study, we describe the sequence, function, and structural evolution of circulating RREs in this patient using plasma samples collected over 6 years of untreated infection. RRE sequence diversity varied over the course of infection, with evidence of selection pressure that led to sequence convergence as disease progressed being found. An increase in RRE functional activity was observed over time, and a key mutation was identified that correlates with a major conformational change in the RRE and increased functional activity. Additional mutations were found that may have contributed to increased activity as a result of greater Shannon entropy in RRE stem-loop II, which is key to primary Rev binding.IMPORTANCE HIV-1 replication requires interaction of the viral Rev protein with a cis-acting regulatory RNA, the Rev response element (RRE), whose sequence changes over time during infection within a single host. In this study, we show that the RRE is subject to selection pressure and that RREs from later time points in infection tend to have higher functional activity. Differences in RRE functional activity are attributable to specific changes in RNA structure. Our results suggest that RRE evolution during infection may be important for HIV pathogenesis and that efforts to develop therapies acting on this viral pathway should take this into account.
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11
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Jayaraman B, Fernandes JD, Yang S, Smith C, Frankel AD. Highly Mutable Linker Regions Regulate HIV-1 Rev Function and Stability. Sci Rep 2019; 9:5139. [PMID: 30914719 PMCID: PMC6435700 DOI: 10.1038/s41598-019-41582-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 03/05/2019] [Indexed: 11/12/2022] Open
Abstract
HIV-1 Rev is an essential viral regulatory protein that facilitates the nuclear export of intron-containing viral mRNAs. It is organized into structured, functionally well-characterized motifs joined by less understood linker regions. Our recent competitive deep mutational scanning study confirmed many known constraints in Rev’s established motifs, but also identified positions of mutational plasticity, most notably in surrounding linker regions. Here, we probe the mutational limits of these linkers by testing the activities of multiple truncation and mass substitution mutations. We find that these regions possess previously unknown structural, functional or regulatory roles, not apparent from systematic point mutational approaches. Specifically, the N- and C-termini of Rev contribute to protein stability; mutations in a turn that connects the two main helices of Rev have different effects in different contexts; and a linker region which connects the second helix of Rev to its nuclear export sequence has structural requirements for function. Thus, Rev function extends beyond its characterized motifs, and is tuned by determinants within seemingly plastic portions of its sequence. Additionally, Rev’s ability to tolerate many of these massive truncations and substitutions illustrates the overall mutational and functional robustness inherent in this viral protein.
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Affiliation(s)
- Bhargavi Jayaraman
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Jason D Fernandes
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, 94158, USA.,UCSC Genomics Institute/Howard Hughes Medical Institute, University of Santa Cruz, Santa Cruz, CA, 95060, USA
| | - Shumin Yang
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, 94158, USA.,School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Cynthia Smith
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Alan D Frankel
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, 94158, USA.
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12
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13
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Faust O, Grunhaus D, Shimshon O, Yavin E, Friedler A. Protein Regulation by Intrinsically Disordered Regions: A Role for Subdomains in the IDR of the HIV-1 Rev Protein. Chembiochem 2018; 19:1618-1624. [PMID: 29791766 DOI: 10.1002/cbic.201800192] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Indexed: 11/06/2022]
Abstract
Intrinsically disordered regions (IDRs) in proteins are highly abundant, but they are still commonly viewed as long stretches of polar, solvent-accessible residues. Here we show that the disordered C-terminal domain (CTD) of HIV-1 Rev has two subregions that carry out two distinct complementary roles of regulating protein oligomerization and contributing to stability. We propose that this takes place through a delicate balance between charged and hydrophobic residues within the IDR. This means that mutations in this region, as well as the known mutations in the structured region of the protein, can affect protein function. We suggest that IDRs in proteins should be divided into subdomains similarly to structured regions, rather than being viewed as long flexible stretches.
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Affiliation(s)
- Ofrah Faust
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Dana Grunhaus
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Odelia Shimshon
- The School of Pharmacy, The Hebrew University of Jerusalem, Hadassah Ein Kerem, Jerusalem, 91120, Israel
| | - Eylon Yavin
- The School of Pharmacy, The Hebrew University of Jerusalem, Hadassah Ein Kerem, Jerusalem, 91120, Israel
| | - Assaf Friedler
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 91904, Israel
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14
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Hammond JA, Zhou L, Lamichhane R, Chu HY, Millar DP, Gerace L, Williamson JR. A Survey of DDX21 Activity During Rev/RRE Complex Formation. J Mol Biol 2018; 430:537-553. [PMID: 28705764 PMCID: PMC5762417 DOI: 10.1016/j.jmb.2017.06.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 06/26/2017] [Accepted: 06/27/2017] [Indexed: 01/17/2023]
Abstract
HIV-1 requires a specialized nuclear export pathway to transport unspliced and partially spliced viral transcripts to the cytoplasm. Central to this pathway is the viral protein Rev, which binds to the Rev response element in stem IIB located on unspliced viral transcripts and subsequently oligomerizes in a cooperative manner. Previous work identified a number of cellular DEAD-box helicases as in vivo binding partners of Rev, and siRNA experiments indicated a functional role for many in the HIV replication cycle. Two DEAD-box proteins, DDX1 and DDX3, had previously been shown to play a role in HIV pathogenesis. In this study, another protein identified in that screen, DDX21, is tested for protein and RNA binding and subsequent enzymatic activities in the context of the Rev/RRE pathway. We found that DDX21 can bind to the RRE with high affinity, and this binding stimulates ATPase activity with an enzymatic efficiency similar to DDX1. Furthermore, DDX21 is both an ATP-dependent and ATP-independent helicase, and both ATPase and ATP-dependent helicase activities are inhibited by Rev in a dose-dependent manner, although ATP-independent helicase activity is not. A conserved binding interaction between DDX protein's DEAD domain and Rev was identified, with Rev's nuclear diffusion inhibitory signal motif playing a significant role in binding. Finally, DDX21 was shown to enhance Rev binding to the RRE in a manner similar to that previously described for DDX1, although DDX3 does not. These data indicate that DDX1 and DDX21 have similar biochemical activities with regard to the Rev/RRE system, while DDX3 differs.
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Affiliation(s)
- John A Hammond
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Li Zhou
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rajan Lamichhane
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hui-Yi Chu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David P Millar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Larry Gerace
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James R Williamson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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15
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Umunnakwe CN, Dorman KS, Dobbs D, Carpenter S. Identification of a homogenous structural basis for oligomerization by retroviral Rev-like proteins. Retrovirology 2017; 14:40. [PMID: 28830558 PMCID: PMC5568270 DOI: 10.1186/s12977-017-0366-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 08/11/2017] [Indexed: 11/17/2022] Open
Abstract
Background Rev-like proteins are post-transcriptional regulatory proteins found in several retrovirus genera, including lentiviruses, betaretroviruses, and deltaretroviruses. These essential proteins mediate the nuclear export of incompletely spliced viral RNA, and act by tethering viral pre-mRNA to the host CRM1 nuclear export machinery. Although all Rev-like proteins are functionally homologous, they share less than 30% sequence identity. In the present study, we computationally assessed the extent of structural homology among retroviral Rev-like proteins within a phylogenetic framework. Results We undertook a comprehensive analysis of overall protein domain architecture and predicted secondary structural features for representative members of the Rev-like family of proteins. Similar patterns of α-helical domains were identified for Rev-like proteins within each genus, with the exception of deltaretroviruses, which were devoid of α-helices. Coiled-coil oligomerization motifs were also identified for most Rev-like proteins, with the notable exceptions of HIV-1, the deltaretroviruses, and some small ruminant lentiviruses. In Rev proteins of primate lentiviruses, the presence of predicted coiled-coil motifs segregated within specific primate lineages: HIV-1 descended from SIVs that lacked predicted coiled-coils in Rev whereas HIV-2 descended from SIVs that contained predicted coiled-coils in Rev. Phylogenetic ancestral reconstruction of coiled-coils for all Rev-like proteins predicted a single origin for the coiled-coil motif, followed by three losses of the predicted signal. The absence of a coiled-coil signal in HIV-1 was associated with replacement of canonical polar residues with non-canonical hydrophobic residues. However, hydrophobic residues were retained in the key ‘a’ and ‘d’ positions, and the α-helical region of HIV-1 Rev oligomerization domain could be modeled as a helical wheel with two predicted interaction interfaces. Moreover, the predicted interfaces mapped to the dimerization and oligomerization interfaces in HIV-1 Rev crystal structures. Helical wheel projections of other retroviral Rev-like proteins, including endogenous sequences, revealed similar interaction interfaces that could mediate oligomerization. Conclusions Sequence-based computational analyses of Rev-like proteins, together with helical wheel projections of oligomerization domains, reveal a conserved homogeneous structural basis for oligomerization by retroviral Rev-like proteins. Electronic supplementary material The online version of this article (doi:10.1186/s12977-017-0366-1) contains supplementary material, which is available to authorized users.
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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, USA.,HIV Dynamics and Replication Program, National Cancer Institute, 1050 Boyles St, Frederick, MD, 21702, USA
| | - Karin S Dorman
- Program in Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA.,Department of Genetics, Developmental and Cell Biology, Iowa State University, Ames, IA, USA.,Department of Statistics, Iowa State University, Ames, IA, USA
| | - Drena Dobbs
- Program in Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA.,Department of Genetics, Developmental and Cell Biology, Iowa State University, Ames, IA, USA
| | - Susan Carpenter
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA.
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16
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Identification and Optimization of Thienopyridine Carboxamides as Inhibitors of HIV Regulatory Complexes. Antimicrob Agents Chemother 2017; 61:AAC.02366-16. [PMID: 28416550 DOI: 10.1128/aac.02366-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 04/06/2017] [Indexed: 12/28/2022] Open
Abstract
Viral regulatory complexes perform critical functions during virus replication and are important targets for therapeutic intervention. In HIV, the Tat and Rev proteins form complexes with multiple viral and cellular factors to direct transcription and export of the viral RNA. These complexes are composed of many proteins and are dynamic, making them difficult to fully recapitulate in vitro Therefore, we developed a cell-based reporter assay to monitor the assembly of viral complexes for inhibitor screening. We screened a small-molecule library and identified multiple hits that inhibit the activity of the viral complexes. A subsequent chemistry effort was focused on a thieno[2,3-b]pyridine scaffold, examples of which inhibited HIV replication and the emergence from viral latency. Notable aspects of the effort to determine the structure-activity relationship (SAR) include migration to the regioisomeric thieno[2,3-c]pyridine ring system and the identification of analogs with single-digit nanomolar activity in both reporter and HIV infectivity assays, an improvement of >100-fold in potency over the original hits. These results validate the screening strategy employed and reveal a promising lead series for the development of a new class of HIV therapeutics.
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17
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Jeong WJ, Kye M, Han SH, Choi JS, Lim YB. Inhibition of Multimolecular RNA-Protein Interactions Using Multitarget-Directed Nanohybrid System. ACS APPLIED MATERIALS & INTERFACES 2017; 9:11537-11545. [PMID: 28287257 DOI: 10.1021/acsami.7b01517] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Multitarget-directed ligands (MTDLs) are hybrid ligands obtained by covalently linking active pharmacophores that can act on different targets. We envision that the concept of MTDLs can also be applied to supramolecular bioinorganic nanohybrid systems. Here, we report the inhibition of multimolecular RNA-protein complexes using multitarget-directed peptide-carbon nanotube hybrids (SPCHs). One of the most well-characterized and important RNA-protein interactions, a Rev-response element (RRE) RNA:Rev protein:Crm1 protein interaction system in human immunodeficiency virus type-1, was used as a model of multimolecular RNA-protein interactions. Although all previous studies have targeted only one of the interaction interfaces, that is, either the RRE:Rev interface or the RRE-Rev complex:Crm1 interface, we here have developed multitarget-directed SPCHs that could target both interfaces because the supramolecular nanosystem could be best suited for inhibiting multimolecular RNA-protein complexes that are characterized by large and complex molecular interfaces. The results showed that the single target-directed SPCHs were inhibitory to the single interface comprised only of RNA and protein in vitro, whereas multitarget-directed SPCHs were inhibitory to the multimolecular RNA-protein interfaces both in vitro and in cellulo. The MTDL nanohybrids represent a novel nanotherapeutic system that could be used to treat complex disease targets.
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Affiliation(s)
- Woo-Jin Jeong
- Department of Materials Science & Engineering, Yonsei University , Seoul 03722, Korea
| | - Mahnseok Kye
- Department of Materials Science & Engineering, Yonsei University , Seoul 03722, Korea
| | - So-Hee Han
- Department of Materials Science & Engineering, Yonsei University , Seoul 03722, Korea
| | - Jun Shik Choi
- Department of Materials Science & Engineering, Yonsei University , Seoul 03722, Korea
| | - Yong-Beom Lim
- Department of Materials Science & Engineering, Yonsei University , Seoul 03722, Korea
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18
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Hammond JA, Lamichhane R, Millar DP, Williamson JR. A DEAD-Box Helicase Mediates an RNA Structural Transition in the HIV-1 Rev Response Element. J Mol Biol 2017; 429:697-714. [PMID: 28153748 PMCID: PMC5510989 DOI: 10.1016/j.jmb.2017.01.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 01/04/2017] [Accepted: 01/21/2017] [Indexed: 01/17/2023]
Abstract
Nuclear export of partially spliced or unspliced HIV-1 RNA transcripts requires binding of the viral protein regulator of expression of virion (Rev) to the Rev response element (RRE) and subsequent oligomerization in a cooperative manner. Cellular DEAD-box helicase DEAD-box protein 1 (DDX1) plays a role in HIV replication, interacting with and affecting Rev-containing HIV transcripts in vivo, interacting directly with the RRE and Rev in vitro, and promoting Rev oligomerization in vitro. Binding of DDX1 results in enhancement of Rev oligomerization on the RRE that is correlated with an RNA structural change within the RRE that persists even after dissociation of DDX1. Furthermore, this structural transition is likely located within the three-way junction of stem II of the RRE that is responsible for initial Rev binding. This discovery of the stem II structural transition leads to a model wherein DDX1 can act as an RNA chaperone, folding stem IIB into a proper Rev binding conformation.
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Affiliation(s)
- John A Hammond
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rajan Lamichhane
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David P Millar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - James R Williamson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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19
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Nuclear Export Signal Masking Regulates HIV-1 Rev Trafficking and Viral RNA Nuclear Export. J Virol 2017; 91:JVI.02107-16. [PMID: 27852860 DOI: 10.1128/jvi.02107-16] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Accepted: 11/14/2016] [Indexed: 12/28/2022] Open
Abstract
HIV-1's Rev protein forms a homo-oligomeric adaptor complex linking viral RNAs to the cellular CRM1/Ran-GTP nuclear export machinery through the activity of Rev's prototypical leucine-rich nuclear export signal (NES). In this study, we used a functional fluorescently tagged Rev fusion protein as a platform to study the effects of modulating Rev NES identity, number, position, or strength on Rev subcellular trafficking, viral RNA nuclear export, and infectious virion production. We found that Rev activity was remarkably tolerant of diverse NES sequences, including supraphysiological NES (SNES) peptides that otherwise arrest CRM1 transport complexes at nuclear pores. Rev's ability to tolerate a SNES was both position and multimerization dependent, an observation consistent with a model wherein Rev self-association acts to transiently mask the NES peptide(s), thereby biasing Rev's trafficking into the nucleus. Combined imaging and functional assays also indicated that NES masking underpins Rev's well-known tendency to accumulate at the nucleolus, as well as Rev's capacity to activate optimal levels of late viral gene expression. We propose that Rev multimerization and NES masking regulates Rev's trafficking to and retention within the nucleus even prior to RNA binding. IMPORTANCE HIV-1 infects more than 34 million people worldwide causing >1 million deaths per year. Infectious virion production is activated by the essential viral Rev protein that mediates nuclear export of intron-bearing late-stage viral mRNAs. Rev's shuttling into and out of the nucleus is regulated by the antagonistic activities of both a peptide-encoded N-terminal nuclear localization signal and C-terminal nuclear export signal (NES). How Rev and related viral proteins balance strong import and export activities in order to achieve optimal levels of viral gene expression is incompletely understood. We provide evidence that multimerization provides a mechanism by which Rev transiently masks its NES peptide, thereby biasing its trafficking to and retention within the nucleus. Targeted pharmacological disruption of Rev-Rev interactions should perturb multiple Rev activities, both Rev-RNA binding and Rev's trafficking to the nucleus in the first place.
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20
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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.
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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.
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21
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Rošić S, Erhardt S. No longer a nuisance: long non-coding RNAs join CENP-A in epigenetic centromere regulation. Cell Mol Life Sci 2016; 73:1387-98. [PMID: 26748759 PMCID: PMC11108473 DOI: 10.1007/s00018-015-2124-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 12/08/2015] [Accepted: 12/17/2015] [Indexed: 01/02/2023]
Abstract
Centromeres represent the basis for kinetochore formation, and are essential for proper chromosome segregation during mitosis. Despite these essential roles, centromeres are not defined by specific DNA sequences, but by epigenetic means. The histone variant CENP-A controls centromere identity epigenetically and is essential for recruiting kinetochore components that attach the chromosomes to the mitotic spindle during mitosis. Recently, a new player in centromere regulation has emerged: long non-coding RNAs transcribed from repetitive regions of centromeric DNA function in regulating centromeres epigenetically. This review summarizes recent findings on the essential roles that transcription, pericentromeric transcripts, and centromere-derived RNAs play in centromere biology.
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Affiliation(s)
- Silvana Rošić
- Medical Research Council Clinical Sciences Centre, Imperial College London, London, UK
| | - Sylvia Erhardt
- ZMBH, DKFZ-ZMBH-Alliance and CellNetworks Excellence Cluster, University of Heidelberg, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany.
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22
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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.
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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
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23
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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.
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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
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24
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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.
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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
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25
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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.
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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
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26
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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.
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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.
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Affiliation(s)
- Ofrah Faust
- Institute of Chemistry, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, Givat Ram 91904, Jerusalem, Israel.
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28
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Abstract
Two new structures shed additional light on the nuclear transport of viral transcripts.
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Affiliation(s)
- James R Williamson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States
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29
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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.
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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.
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30
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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.
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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
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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
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31
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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.
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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
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32
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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]
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33
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Devi G, Zhou Y, Zhong Z, Toh DFK, Chen G. RNA triplexes: from structural principles to biological and biotech applications. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 6:111-28. [DOI: 10.1002/wrna.1261] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 06/30/2014] [Accepted: 07/14/2014] [Indexed: 12/29/2022]
Affiliation(s)
- Gitali Devi
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore Singapore
| | - Yuan Zhou
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore Singapore
| | - Zhensheng Zhong
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore Singapore
| | - Desiree-Faye Kaixin Toh
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore Singapore
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences; Nanyang Technological University; Singapore Singapore
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34
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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.
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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
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35
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Zhuang X, Stahl SJ, Watts NR, DiMattia MA, Steven AC, Wingfield PT. A cell-penetrating antibody fragment against HIV-1 Rev has high antiviral activity: characterization of the paratope. J Biol Chem 2014; 289:20222-33. [PMID: 24878961 DOI: 10.1074/jbc.m114.581090] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The HIV-1 protein Rev oligomerizes on viral transcripts and directs their nuclear export. Previously, a Fab against Rev generated by phage display was used to crystallize and solve the structure of the Rev oligomerization domain. Here we have investigated the capability of this Fab to block Rev oligomerization and inhibit HIV-1 replication. The Fab itself did not have antiviral activity, but when a Tat-derived cell-penetrating peptide was appended, the resulting molecule (FabRev1-Tat) was strongly inhibitory of three different CCR5-tropic HIV-1 isolates (IC50 = 0.09-0.44 μg/ml), as assessed by suppression of reverse transcriptase activity in infected peripheral blood mononuclear cells, and had low cell toxicity (TC50 > 100 μg/ml). FabRev1-Tat was taken up by both peripheral blood mononuclear and HEK293T cells, appearing in both the cytoplasm and nucleus, as shown by immunofluorescence confocal laser scanning microscopy. Computational alanine scanning was used to identify key residues in the complementarity-determining regions to guide mutagenesis experiments. Residues in the light chain CDR3 (LCDR3) were assessed to be important. Residues in LCDR3 were mutated, and LCDR3-Tyr(92) was found to be critical for binding to Rev, as judged by surface plasmon resonance and electron microscopy. Peptides corresponding to all six CDR regions were synthesized and tested for Rev binding. None of the linear peptides had significant affinity for Rev, but four of the amide-cyclic forms did. Especially cyclic-LCDR3 (LGGYPAASYRTA) had high affinity for Rev and was able to effectively depolymerize Rev filaments, as shown by both surface plasmon resonance and electron microscopy.
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Affiliation(s)
| | | | | | - Michael A DiMattia
- the Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Alasdair C Steven
- the Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892
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36
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Casu F, Duggan BM, Hennig M. The arginine-rich RNA-binding motif of HIV-1 Rev is intrinsically disordered and folds upon RRE binding. Biophys J 2014; 105:1004-17. [PMID: 23972852 DOI: 10.1016/j.bpj.2013.07.022] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 06/19/2013] [Accepted: 07/02/2013] [Indexed: 11/17/2022] Open
Abstract
Arginine-rich motifs (ARMs) capable of binding diverse RNA structures play critical roles in transcription, translation, RNA trafficking, and RNA packaging. The regulatory HIV-1 protein Rev is essential for viral replication and belongs to the ARM family of RNA-binding proteins. During the early stages of the HIV-1 life cycle, incompletely spliced and full-length viral mRNAs are very inefficiently recognized by the splicing machinery of the host cell and are subject to degradation in the cell nucleus. These transcripts harbor the Rev Response Element (RRE), which orchestrates the interaction with the Rev ARM and the successive Rev-dependent mRNA export pathway. Based on established criteria for predicting intrinsic disorder, such as hydropathy, combined with significant net charge, the very basic primary sequences of ARMs are expected to adopt coil-like structures. Thus, we initiated this study to investigate the conformational changes of the Rev ARM associated with RNA binding. We used multidimensional NMR and circular dichroism spectroscopy to monitor the observed structural transitions, and described the conformational landscapes using statistical ensemble and molecular-dynamics simulations. The combined spectroscopic and simulated results imply that the Rev ARM is intrinsically disordered not only as an isolated peptide but also when it is embedded into an oligomerization-deficient Rev mutant. RRE recognition triggers a crucial coil-to-helix transition employing an induced-fit mechanism.
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Affiliation(s)
- Fabio Casu
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
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37
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Lusvarghi S, Sztuba-Solinska J, Purzycka KJ, Pauly GT, Rausch JW, Grice SFJL. The HIV-2 Rev-response element: determining secondary structure and defining folding intermediates. Nucleic Acids Res 2013; 41:6637-49. [PMID: 23640333 PMCID: PMC3711434 DOI: 10.1093/nar/gkt353] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Interaction between the viral protein Rev and the RNA motifs known as Rev response elements (RREs) is required for transport of unspliced and partially spliced human immunodeficiency virus (HIV)-1 and HIV-2 RNAs from the nucleus to the cytoplasm during the later stages of virus replication. A more detailed understanding of these nucleoprotein complexes and the host factors with which they interact should accelerate the development of new antiviral drugs targeting cis-acting RNA regulatory signals. In this communication, the secondary structures of the HIV-2 RRE and two RNA folding precursors have been identified using the SHAPE (selective 2′-hydroxyl acylation analyzed by primer extension) chemical probing methodology together with a novel mathematical approach for determining the secondary structures of RNA conformers present in a mixture. A complementary chemical probing technique was also used to support these secondary structure models, to confirm that the RRE2 RNA undergoes a folding transition and to obtain information about the relative positioning of RRE2 substructures in three dimensions. Our analysis collectively suggests that the HIV-2 RRE undergoes two conformational transitions before assuming the energetically most favorable conformer. The 3D models for the HIV-2 RRE and folding intermediates are also presented, wherein the Rev-binding stem–loops (IIB and I) are located coaxially in the former, which is in agreement with previous models for HIV-1 Rev-RRE binding.
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Affiliation(s)
- Sabrina Lusvarghi
- HIV Drug Resistance Program, Reverse Transcriptase Biochemistry Section, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
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38
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Han SH, Lee MK, Lim YB. Bioinspired Self-Assembled Peptide Nanofibers with Thermostable Multivalent α-Helices. Biomacromolecules 2013; 14:1594-9. [DOI: 10.1021/bm400233x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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
| | - Mun-kyung Lee
- Translational Research Center for Protein
Function Control and Department of Materials
Science and Engineering, Yonsei University, Seoul 120-749, Korea
| | - Yong-beom Lim
- Translational Research Center for Protein
Function Control and Department of Materials
Science and Engineering, Yonsei University, Seoul 120-749, Korea
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39
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Vercruysse T, Boons E, Venken T, Vanstreels E, Voet A, Steyaert J, De Maeyer M, Daelemans D. Mapping the binding interface between an HIV-1 inhibiting intrabody and the viral protein Rev. PLoS One 2013; 8:e60259. [PMID: 23565213 PMCID: PMC3615019 DOI: 10.1371/journal.pone.0060259] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 02/24/2013] [Indexed: 11/19/2022] Open
Abstract
HIV-1 Rev is the key protein in the nucleocytoplasmic export and expression of the late viral mRNAs. An important aspect for its function is its ability to multimerize on these mRNAs. We have recently identified a llama single-domain antibody (Nb190) as the first inhibitor targeting the Rev multimerization function in cells. This nanobody is a potent intracellular antibody that efficiently inhibits HIV-1 viral production. In order to gain insight into the Nb190-Rev interaction interface, we performed mutational and docking studies to map the interface between the nanobody paratope and the Rev epitope. Alanine mutants of the hyper-variable domains of Nb190 and the Rev multimerization domains were evaluated in different assays measuring Nb190-Rev interaction or viral production. Seven residues within Nb190 and five Rev residues are demonstrated to be crucial for epitope recognition. These experimental data were used to perform docking experiments and map the Nb190-Rev structural interface. This Nb190-Rev interaction model can guide further studies of the Nb190 effect on HIV-1 Rev function and could serve as starting point for the rational development of smaller entities binding to the Nb190 epitope, aimed at interfering with protein-protein interactions of the Rev N-terminal domain.
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Affiliation(s)
| | - Eline Boons
- Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Tom Venken
- Division of Biochemistry, Molecular and Structural Biology, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Els Vanstreels
- Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Arnout Voet
- Division of Biochemistry, Molecular and Structural Biology, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Jan Steyaert
- Structural Biology Brussel Laboratory, Department of Molecular Interactions, Vrije Universiteit Brussel, Brussels, Belgium
| | - Marc De Maeyer
- Division of Biochemistry, Molecular and Structural Biology, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Dirk Daelemans
- Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
- * E-mail:
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40
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Han S, Kim D, Han SH, Kim NH, Kim SH, Lim YB. Structural and Conformational Dynamics of Self-Assembling Bioactive β-Sheet Peptide Nanostructures Decorated with Multivalent RNA-Binding Peptides. J Am Chem Soc 2012; 134:16047-53. [DOI: 10.1021/ja307493t] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Sanghun Han
- Translational Research Center for Protein Function Control and Department of Materials Science & Engineering, Yonsei University, Seoul 120-749, Korea
| | - Donghun Kim
- Division of Materials
Science, Korea Basic Science Institute (KBSI), Daejeon 305-333,
Korea
| | - So-hee Han
- Translational Research Center for Protein Function Control and Department of Materials Science & Engineering, Yonsei University, Seoul 120-749, Korea
| | - Nam Hee Kim
- Division of Materials
Science, Korea Basic Science Institute (KBSI), Daejeon 305-333,
Korea
| | - Sun Hee Kim
- Division of Materials
Science, Korea Basic Science Institute (KBSI), Daejeon 305-333,
Korea
| | - Yong-beom Lim
- Translational Research Center for Protein Function Control and Department of Materials Science & Engineering, Yonsei University, Seoul 120-749, Korea
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41
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Hoffmann D, Schwarck D, Banning C, Brenner M, Mariyanna L, Krepstakies M, Schindler M, Millar DP, Hauber J. Formation of trans-activation competent HIV-1 Rev:RRE complexes requires the recruitment of multiple protein activation domains. PLoS One 2012; 7:e38305. [PMID: 22675540 PMCID: PMC3366918 DOI: 10.1371/journal.pone.0038305] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 05/07/2012] [Indexed: 12/13/2022] Open
Abstract
The HIV-1 Rev trans-activator is a nucleocytoplasmic shuttle protein that is essential for virus replication. Rev directly binds to unspliced and incompletely spliced viral RNA via the cis-acting Rev Response Element (RRE) sequence. Subsequently, Rev oligomerizes cooperatively and interacts with the cellular nuclear export receptor CRM1. In addition to mediating nuclear RNA export, Rev also affects the stability, translation and packaging of Rev-bound viral transcripts. Although it is established that Rev function requires the multimeric assembly of Rev molecules on the RRE, relatively little is known about how many Rev monomers are sufficient to form a trans-activation competent Rev:RRE complex, or which specific activity of Rev is affected by its oligomerization. We here analyzed by functional studies how homooligomer formation of Rev affects the trans-activation capacity of this essential HIV-1 regulatory protein. In a gain-of-function approach, we fused various heterologous dimerization domains to an otherwise oligomerization-defective Rev mutant and were able to demonstrate that oligomerization of Rev is not required per se for the nuclear export of this viral trans-activator. In contrast, however, the formation of Rev oligomers on the RRE is a precondition to trans-activation by directly affecting the nuclear export of Rev-regulated mRNA. Moreover, experimental evidence is provided showing that at least two protein activation domains are required for the formation of trans-activation competent Rev:RRE complexes. The presented data further refine the model of Rev trans-activation by directly demonstrating that Rev oligomerization on the RRE, thereby recruiting at least two protein activation domains, is required for nuclear export of unspliced and incompletely spliced viral RNA.
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Affiliation(s)
- Dirk Hoffmann
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Doreen Schwarck
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Carina Banning
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Matthias Brenner
- Institute for Clinical and Molecular Virology, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Lakshmikanth Mariyanna
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Marcel Krepstakies
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Michael Schindler
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - David P. Millar
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Joachim Hauber
- Heinrich Pette Institute – Leibniz Institute for Experimental Virology, Hamburg, Germany
- * E-mail:
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Shida H. Role of Nucleocytoplasmic RNA Transport during the Life Cycle of Retroviruses. Front Microbiol 2012; 3:179. [PMID: 22783232 PMCID: PMC3390767 DOI: 10.3389/fmicb.2012.00179] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 04/26/2012] [Indexed: 12/14/2022] Open
Abstract
Retroviruses have evolved mechanisms for transporting their intron-containing RNAs (including genomic and messenger RNAs, which encode virion components) from the nucleus to the cytoplasm of the infected cell. Human retroviruses, such as human immunodeficiency virus (HIV) and human T cell leukemia virus type 1 (HTLV-1), encode the regulatory proteins Rev and Rex, which form a bridge between the viral RNA and the export receptor CRM1. Recent studies show that these transport systems are not only involved in RNA export, but also in the encapsidation of genomic RNA; furthermore, they influence subsequent events in the cytoplasm, including the translation of the cognate mRNA, transport of Gag proteins to the plasma membrane, and the formation of virus particles. Moreover, the mode of interaction between the viral and cellular RNA transport machinery underlies the species-specific propagation of HIV-1 and HTLV-1, forming the basis for constructing animal models of infection. This review article discusses recent progress regarding these issues.
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Affiliation(s)
- Hisatoshi Shida
- Division of Molecular Virology, Institute of Immunological Science, Hokkaido University Sapporo, Japan
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Venken T, Daelemans D, De Maeyer M, Voet A. Computational investigation of the HIV-1 Rev multimerization using molecular dynamics simulations and binding free energy calculations. Proteins 2012; 80:1633-46. [PMID: 22447650 DOI: 10.1002/prot.24057] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 01/06/2012] [Accepted: 02/06/2012] [Indexed: 01/01/2023]
Abstract
The HIV Rev protein mediates the nuclear export of viral mRNA, and is thereby essential for the production of late viral proteins in the replication cycle. Rev forms a large organized multimeric protein-protein complex for proper functioning. Recently, the three-dimensional structures of a Rev dimer and tetramer have been resolved and provide the basis for a thorough structural analysis of the binding interaction. Here, molecular dynamics (MD) and binding free energy calculations were performed to elucidate the forces thriving dimerization and higher order multimerization of the Rev protein. It is found that despite the structural differences between each crystal structure, both display a similar behavior according to our calculations. Our analysis based on a molecular mechanics-generalized Born surface area (MM/GBSA) and a configurational entropy approach demonstrates that the higher order multimerization site is much weaker than the dimerization site. In addition, a quantitative hot spot analysis combined with a mutational analysis reveals the most contributing amino acid residues for protein interactions in agreement with experimental results. Additional residues were found in each interface, which are important for the protein interaction. The investigation of the thermodynamics of the Rev multimerization interactions performed here could be a further step in the development of novel antiretrovirals using structure based drug design. Moreover, the variability of the angle between each Rev monomer as measured during the MD simulations suggests a role of the Rev protein in allowing flexibility of the arginine rich domain (ARM) to accommodate RNA binding.
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Affiliation(s)
- Tom Venken
- Laboratory for Biomolecular Modelling and BioMacS, Department of Chemistry, Division of Biochemistry, Molecular and Structural Biology, KULeuven, Heverlee, Belgium
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Abstract
Three-dimensional molecular structures can provide detailed information on biological mechanisms and, for cases in which the molecular function affects human health, can significantly aid in the development of therapeutic interventions. For almost 25 years, key components of the lentivirus HIV-1, including the envelope glycoproteins, the capsid and the replication enzymes reverse transcriptase, integrase and protease, have been scrutinized to near atomic-scale resolution. Moreover, structural analyses of the interactions between viral and host cell components have yielded key insights into the mechanisms of viral entry, chromosomal integration, transcription and egress from cells. Here, we review recent advances in HIV-1 structural biology, focusing on the molecular mechanisms of viral replication and on the development of new therapeutics.
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45
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Abstract
It has been known for some time that the HIV Rev protein binds and oligomerizes on a well-defined multiple stem-loop RNA structure, named the Rev Response Element (RRE), which is present in a subset of HIV mRNAs. This binding is the first step in a pathway that overcomes a host restriction, which would otherwise prevent the export of these RNAs to the cytoplasm. Four recent publications now provide new insight into the structure of Rev and the multimeric RNA-protein complex that forms on the RRE [1–4]. Two unexpected and remarkable findings revealed in these studies are the flexibility of RNA binding that is demonstrated by the Rev arginine-rich RNA binding motif, and the way that both Rev protein and RRE contribute to the formation of the complex in a highly cooperative fashion. These studies also define the Rev dimerization and oligomerization interfaces to a resolution of 2.5Å, providing a framework necessary for further structural and functional studies. Additionally, and perhaps most importantly, they also pave the way for rational drug design, which may ultimately lead to new therapies to inhibit this essential HIV function.
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Allard SD, de Goede AL, De Keersmaecker B, Heirman C, Lacor P, Osterhaus ADME, Demanet C, Thielemans K, Gruters RA, Aerts JL. Sequence evolution and escape from specific immune pressure of an HIV-1 Rev epitope with extensive sequence similarity to human nucleolar protein 6. ACTA ACUST UNITED AC 2012; 79:174-85. [DOI: 10.1111/j.1399-0039.2012.01837.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Fernandes J, Jayaraman B, Frankel A. The HIV-1 Rev response element: an RNA scaffold that directs the cooperative assembly of a homo-oligomeric ribonucleoprotein complex. RNA Biol 2012; 9:6-11. [PMID: 22258145 PMCID: PMC3342944 DOI: 10.4161/rna.9.1.18178] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The HIV-1 Rev response element (RRE) is a ~350 nucleotide, highly structured, cis-acting RNA element essential for viral replication. It is located in the env coding region of the viral genome and is extremely well conserved across different HIV-1 isolates. It is present on all partially spliced and unspliced viral mRNA transcripts, and serves as an RNA framework onto which multiple molecules of the viral protein Rev assemble. The Rev-RRE oligomeric complex mediates the export of these messages from the nucleus to the cytoplasm, where they are translated to produce essential viral proteins and/or packaged as genomes for new virions.
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Affiliation(s)
- Jason Fernandes
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
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Edgcomb SP, Carmel AB, Naji S, Ambrus-Aikelin G, Reyes JR, Saphire ACS, Gerace L, Williamson JR. DDX1 is an RNA-dependent ATPase involved in HIV-1 Rev function and virus replication. J Mol Biol 2011; 415:61-74. [PMID: 22051512 PMCID: PMC3249508 DOI: 10.1016/j.jmb.2011.10.032] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 10/18/2011] [Accepted: 10/18/2011] [Indexed: 12/26/2022]
Abstract
The human immunodeficiency virus type 1 (HIV-1) Rev protein is essential for the virus because it promotes nuclear export of alternatively processed mRNAs, and Rev is also linked to translation of viral mRNAs and genome encapsidation. Previously, the human DEAD-box helicase DDX1 was suggested to be involved in Rev functions, but this relationship is not well understood. Biochemical studies of DDX1 and its interactions with Rev and model RNA oligonucleotides were carried out to investigate the molecular basis for association of these components. A combination of gel-filtration chromatography and circular dichroism spectroscopy demonstrated that recombinant DDX1 expressed in Escherichia coli is a well-behaved folded protein. Binding assays using fluorescently labeled Rev and cell-based immunoprecipitation analysis confirmed a specific RNA-independent DDX1–Rev interaction. Additionally, DDX1 was shown to be an RNA-activated ATPase, wherein Rev-bound RNA was equally effective at stimulating ATPase activity as protein-free RNA. Gel mobility shift assays further demonstrated that DDX1 forms complexes with Rev-bound RNA. RNA silencing of DDX1 provided strong evidence that DDX1 is required for both Rev activity and HIV production from infected cells. Collectively, these studies demonstrate a clear link between DDX1 and HIV-1 Rev in cell-based assays of HIV-1 production and provide the first demonstration that recombinant DDX1 binds Rev and RNA and has RNA-dependent catalytic activity.
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Affiliation(s)
- Stephen P Edgcomb
- Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Vercruysse T, Pawar S, De Borggraeve W, Pardon E, Pavlakis GN, Pannecouque C, Steyaert J, Balzarini J, Daelemans D. Measuring cooperative Rev protein-protein interactions on Rev responsive RNA by fluorescence resonance energy transfer. RNA Biol 2011; 8:316-24. [PMID: 21358282 DOI: 10.4161/rna.8.2.13782] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The export of viral RNA from the nucleus to the cytoplasm of the cellular host is a crucial step in the life cycle of HIV-1 that is mediated by the viral Rev protein. One aspect of the Rev function, its multimerization, is still unexplored as a target for antiviral therapy. This is partly due to the lack of a fast and solid system to measure Rev multimerization. We have developed a high throughput in vitro Rev multimerization assay based on fluorescence resonance energy transfer (FRET) in which real-time Rev-Rev interactions can be measured both in the absence and the presence of Rev specific RRE RNA. Well-characterized Rev multimerization deficient mutants showed reduced FRET as well as unlabeled Rev molecules were able to inhibit the FRET signal demonstrating the specificity of the assay. Upon multimerization along RRE RNA the FRET signal significantly increased but dropped again at equimolar Rev/RRE ratios suggesting that in this condition most Rev molecules are bound as monomers to the RRE. Furthermore, using this assay, we demonstrate that a previously selected llama heavy-chain only antibody was shown to not only prevent the development of Rev multimers but also disassemble the already formed complexes confirming the dynamic nature of the Rev-Rev interactions. The in vitro FRET based multimerization assay facilitates the further study of the basic mechanism of cooperative Rev multimerization along the RRE and is also widely applicable to study the assembly of other functional complexes involving protein homo-multimerization or cooperative protein-protein interactions on RNA or DNA.
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Affiliation(s)
- Thomas Vercruysse
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
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Single-nucleotide changes in the HIV Rev-response element mediate resistance to compounds that inhibit Rev function. J Virol 2011; 85:3940-9. [PMID: 21289114 DOI: 10.1128/jvi.02683-10] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Previously we described the identification of two compounds (3-amino-5-ethyl-4,6-dimethylthieno[2,3-b]pyridine-2-carboxamide [103833] and 4-amino-6-methoxy-2-(trifluoromethyl)-3-quinolinecarbonitrile [104366]) that interfered with HIV replication through the inhibition of Rev function. We now describe resistant viral variants that arose after drug selection, using virus derived from two different HIV proviral clones, NL4-3 and R7/3. With HIV(NL4-3), each compound selected a different single point mutation in the Rev response element (RRE) at the bottom of stem-loop IIC. Either mutation led to the lengthening of the stem-loop IIC stem by an additional base pair, creating an RRE that was more responsive to lower concentrations of Rev than the wild type. Surprisingly, wild-type HIV(R7/3) was also found to be inhibited when tested with these compounds, in spite of the fact this virus already has an RNA stem-loop IIC similar to the one in the resistant NL4-3 variant. When drug resistance was selected in HIV(R7/3), a virus arose with two nucleotide changes that mapped to the envelope region outside the RRE. One of these nucleotide changes was synonymous with respect to env, and one was not. The combination of both nucleotide changes appeared to be necessary for the resistance phenotype as the individual point mutations by themselves did not convey resistance. Thus, although drug-resistant variants can be generated with both viral strains, the underlying mechanism is clearly different. These results highlight that minor nucleotide changes in HIV RNA, outside the primary Rev binding site, can significantly alter the efficiency of the Rev/RRE pathway.
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