1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Behrens RT, Sherer NM. Retroviral hijacking of host transport pathways for genome nuclear export. mBio 2023; 14:e0007023. [PMID: 37909783 PMCID: PMC10746203 DOI: 10.1128/mbio.00070-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
Recent advances in the study of virus-cell interactions have improved our understanding of how viruses that replicate their genomes in the nucleus (e.g., retroviruses, hepadnaviruses, herpesviruses, and a subset of RNA viruses) hijack cellular pathways to export these genomes to the cytoplasm where they access virion egress pathways. These findings shed light on novel aspects of viral life cycles relevant to the development of new antiviral strategies and can yield new tractable, virus-based tools for exposing additional secrets of the cell. The goal of this review is to summarize defined and emerging modes of virus-host interactions that drive the transit of viral genomes out of the nucleus across the nuclear envelope barrier, with an emphasis on retroviruses that are most extensively studied. In this context, we prioritize discussion of recent progress in understanding the trafficking and function of the human immunodeficiency virus type 1 Rev protein, exemplifying a relatively refined example of stepwise, cooperativity-driven viral subversion of multi-subunit host transport receptor complexes.
Collapse
Affiliation(s)
- Ryan T. Behrens
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - Nathan M. Sherer
- McArdle Laboratory for Cancer Research and Carbone Cancer Center, University of Wisconsin, Madison, Wisconsin, USA
- Institute for Molecular Virology, University of Wisconsin, Madison, Wisconsin, USA
| |
Collapse
|
3
|
Wang Y, Ling X, Zhang C, Zou J, Luo B, Luo Y, Jia X, Jia G, Zhang M, Hu J, Liu T, Wang Y, Lu K, Li D, Ma J, Liu C, Su Z. Modular characterization of SARS-CoV-2 nucleocapsid protein domain functions in nucleocapsid-like assembly. MOLECULAR BIOMEDICINE 2023; 4:16. [PMID: 37211575 DOI: 10.1186/s43556-023-00129-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/09/2023] [Indexed: 05/23/2023] Open
Abstract
SARS-CoV-2 and its variants, with the Omicron subvariant XBB currently prevailing the global infections, continue to pose threats on public health worldwide. This non-segmented positive-stranded RNA virus encodes the multi-functional nucleocapsid protein (N) that plays key roles in viral infection, replication, genome packaging and budding. N protein consists of two structural domains, NTD and CTD, and three intrinsically disordered regions (IDRs) including the NIDR, the serine/arginine rich motif (SRIDR), and the CIDR. Previous studies revealed functions of N protein in RNA binding, oligomerization, and liquid-liquid phase separation (LLPS), however, characterizations of individual domains and their dissected contributions to N protein functions remain incomplete. In particular, little is known about N protein assembly that may play essential roles in viral replication and genome packing. Here, we present a modular approach to dissect functional roles of individual domains in SARS-CoV-2 N protein that reveals inhibitory or augmented modulations of protein assembly and LLPS in the presence of viral RNAs. Intriguingly, full-length N protein (NFL) assembles into ring-like architecture whereas the truncated SRIDR-CTD-CIDR (N182-419) promotes filamentous assembly. Moreover, LLPS droplets of NFL and N182-419 are significantly enlarged in the presence of viral RNAs, and we observed filamentous structures in the N182-419 droplets using correlative light and electron microscopy (CLEM), suggesting that the formation of LLPS droplets may promote higher-order assembly of N protein for transcription, replication and packaging. Together this study expands our understanding of the multiple functions of N protein in SARS-CoV-2.
Collapse
Affiliation(s)
- Yan Wang
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Xiaobin Ling
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Chong Zhang
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Jian Zou
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Bingnan Luo
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Yongbo Luo
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Xinyu Jia
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Guowen Jia
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Minghua Zhang
- College of Polymer Science and Engineering, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Junchao Hu
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Ting Liu
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Yuanfeiyi Wang
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Kefeng Lu
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Dan Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| | - Cong Liu
- Interdisciplinary Research Center On Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China.
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Zhaoming Su
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China.
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
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]
|
6
|
Liu R, Xia S, Li H. Native top-down mass spectrometry for higher-order structural characterization of proteins and complexes. MASS SPECTROMETRY REVIEWS 2022:e21793. [PMID: 35757976 DOI: 10.1002/mas.21793] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Progress in structural biology research has led to a high demand for powerful and yet complementary analytical tools for structural characterization of proteins and protein complexes. This demand has significantly increased interest in native mass spectrometry (nMS), particularly native top-down mass spectrometry (nTDMS) in the past decade. This review highlights recent advances in nTDMS for structural research of biological assemblies, with a particular focus on the extra multi-layers of information enabled by TDMS. We include a short introduction of sample preparation and ionization to nMS, tandem fragmentation techniques as well as mass analyzers and software/analysis pipelines used for nTDMS. We highlight unique structural information offered by nTDMS and examples of its broad range of applications in proteins, protein-ligand interactions (metal, cofactor/drug, DNA/RNA, and protein), therapeutic antibodies and antigen-antibody complexes, membrane proteins, macromolecular machineries (ribosome, nucleosome, proteosome, and viruses), to endogenous protein complexes. The challenges, potential, along with perspectives of nTDMS methods for the analysis of proteins and protein assemblies in recombinant and biological samples are discussed.
Collapse
Affiliation(s)
- Ruijie Liu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shujun Xia
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Huilin Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Abstract
The human immunodeficiency virus type 1 (HIV-1) proteome is expressed from alternatively spliced and unspliced genomic RNAs. However, HIV-1 RNAs that are not fully spliced are perceived by the host machinery as defective and are retained in the nucleus. During late infection, HIV-1 bypasses this regulatory mechanism by expression of the Rev protein from a fully spliced mRNA. Once imported into the nucleus, Rev mediates the export of unprocessed HIV-1 RNAs to the cytoplasm, leading to the production of the viral progeny. While regarded as a canonical RNA export factor, Rev has also been linked to HIV-1 RNA translation, stabilization, splicing and packaging. However, Rev's functions beyond RNA export have remained poorly understood. Here, we revisit this paradigmatic protein, reviewing recent data investigating its structure and function. We conclude by asking: what remains unknown about this enigmatic viral protein?
Collapse
Affiliation(s)
| | - Aino Järvelin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Ilan Davis
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Alfredo Castello
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, 464 Bearsden Road, Glasgow G61 1QH, UK
| |
Collapse
|
10
|
Native mass spectrometry reveals the initial binding events of HIV-1 rev to RRE stem II RNA. Nat Commun 2020; 11:5750. [PMID: 33188169 PMCID: PMC7666190 DOI: 10.1038/s41467-020-19144-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 09/29/2020] [Indexed: 11/24/2022] Open
Abstract
Nuclear export complexes composed of rev response element (RRE) ribonucleic acid (RNA) and multiple molecules of rev protein are promising targets for the development of therapeutic strategies against human immunodeficiency virus type 1 (HIV-1), but their assembly remains poorly understood. Using native mass spectrometry, we show here that rev initially binds to the upper stem of RRE IIB, from where it is relayed to binding sites that allow for rev dimerization. The newly discovered binding region implies initial rev recognition by nucleotides that are not part of the internal loop of RRE stem IIB RNA, which was previously identified as the preferred binding region. Our study highlights the unique capability of native mass spectrometry to separately study the binding interfaces of RNA/protein complexes of different stoichiometry, and provides a detailed understanding of the mechanism of RRE/rev association with implications for the rational design of potential drugs against HIV-1 infection. The HIV-1 RNA-binding protein rev facilitates nuclear export of viral RNA. Here, the authors use native mass spectrometry to study the interactions between rev-derived peptides and rev response elements of HIV-1 RNA, providing mechanistic insights into rev recognition and recruitment.
Collapse
|
11
|
Chu CC, Liu B, Plangger R, Kreutz C, Al-Hashimi HM. m6A minimally impacts the structure, dynamics, and Rev ARM binding properties of HIV-1 RRE stem IIB. PLoS One 2019; 14:e0224850. [PMID: 31825959 PMCID: PMC6905585 DOI: 10.1371/journal.pone.0224850] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 11/26/2019] [Indexed: 02/02/2023] Open
Abstract
N6-methyladenosine (m6A) is a ubiquitous RNA post-transcriptional modification found in coding as well as non-coding RNAs. m6A has also been found in viral RNAs where it is proposed to modulate host-pathogen interactions. Two m6A sites have been reported in the HIV-1 Rev response element (RRE) stem IIB, one of which was shown to enhance binding to the viral protein Rev and viral RNA export. However, because these m6A sites have not been observed in other studies mapping m6A in HIV-1 RNA, their significance remains to be firmly established. Here, using optical melting experiments, NMR spectroscopy, and in vitro binding assays, we show that m6A minimally impacts the stability, structure, and dynamics of RRE stem IIB as well as its binding affinity to the Rev arginine-rich-motif (ARM) in vitro. Our results indicate that if present in stem IIB, m6A is unlikely to substantially alter the conformational properties of the RNA. Our results add to a growing view that the impact of m6A on RNA depends on sequence context and Mg2+.
Collapse
Affiliation(s)
- Chia-Chieh Chu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States of America
| | - Bei Liu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States of America
| | - Raphael Plangger
- Institute of Organic Chemistry and Center for Molecular Biosciences CMBI, Universität Innsbruck, Innsbruck, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences CMBI, Universität Innsbruck, Innsbruck, Austria
| | - Hashim M. Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, United States of America
- Department of Chemistry, Duke University, Durham, NC, United States of America
| |
Collapse
|
12
|
Chu CC, Plangger R, Kreutz C, Al-Hashimi HM. Dynamic ensemble of HIV-1 RRE stem IIB reveals non-native conformations that disrupt the Rev-binding site. Nucleic Acids Res 2019; 47:7105-7117. [PMID: 31199872 PMCID: PMC6649712 DOI: 10.1093/nar/gkz498] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 05/21/2019] [Accepted: 06/07/2019] [Indexed: 01/01/2023] Open
Abstract
The HIV-1 Rev response element (RRE) RNA element mediates the nuclear export of intron containing viral RNAs by forming an oligomeric complex with the viral protein Rev. Stem IIB and nearby stem II three-way junction nucleate oligomerization through cooperative binding of two Rev molecules. Conformational flexibility at this RRE region has been shown to be important for Rev binding. However, the nature of the flexibility has remained elusive. Here, using NMR relaxation dispersion, including a new strategy for directly observing transient conformational states in large RNAs, we find that stem IIB alone or when part of the larger RREII three-way junction robustly exists in dynamic equilibrium with non-native excited state (ES) conformations that have a combined population of ∼20%. The ESs disrupt the Rev-binding site by changing local secondary structure, and their stabilization via point substitution mutations decreases the binding affinity to the Rev arginine-rich motif (ARM) by 15- to 80-fold. The ensemble clarifies the conformational flexibility observed in stem IIB, reveals long-range conformational coupling between stem IIB and the three-way junction that may play roles in cooperative Rev binding, and also identifies non-native RRE conformational states as new targets for the development of anti-HIV therapeutics.
Collapse
Affiliation(s)
- Chia-Chieh Chu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Raphael Plangger
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Universität Innsbruck, 6020 Innsbruck, Austria
| | - Christoph Kreutz
- Institute of Organic Chemistry and Center for Molecular Biosciences (CMBI), Universität Innsbruck, 6020 Innsbruck, Austria
| | - Hashim M Al-Hashimi
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Chemistry, Duke University, Durham, NC 27708, USA
| |
Collapse
|
13
|
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.
Collapse
|
14
|
Rausch JW, Sztuba-Solinska J, Le Grice SFJ. Probing the Structures of Viral RNA Regulatory Elements with SHAPE and Related Methodologies. Front Microbiol 2018; 8:2634. [PMID: 29375504 PMCID: PMC5767303 DOI: 10.3389/fmicb.2017.02634] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 12/18/2017] [Indexed: 01/18/2023] Open
Abstract
Viral RNAs were selected by evolution to possess maximum functionality in a minimal sequence. Depending on the classification of the virus and the type of RNA in question, viral RNAs must alternately be replicated, spliced, transcribed, transported from the nucleus into the cytoplasm, translated and/or packaged into nascent virions, and in most cases, provide the sequence and structural determinants to facilitate these processes. One consequence of this compact multifunctionality is that viral RNA structures can be exquisitely complex, often involving intermolecular interactions with RNA or protein, intramolecular interactions between sequence segments separated by several thousands of nucleotides, or specialized motifs such as pseudoknots or kissing loops. The fluidity of viral RNA structure can also present a challenge when attempting to characterize it, as genomic RNAs especially are likely to sample numerous conformations at various stages of the virus life cycle. Here we review advances in chemoenzymatic structure probing that have made it possible to address such challenges with respect to cis-acting elements, full-length viral genomes and long non-coding RNAs that play a major role in regulating viral gene expression.
Collapse
Affiliation(s)
- Jason W Rausch
- Basic Research Laboratory, National Cancer Institute, Frederick, MD, United States
| | - Joanna Sztuba-Solinska
- Basic Research Laboratory, National Cancer Institute, Frederick, MD, United States.,Department of Biological Sciences, Auburn University, Auburn, AL, United States
| | - Stuart F J Le Grice
- Basic Research Laboratory, National Cancer Institute, Frederick, MD, United States
| |
Collapse
|
15
|
Yue Y, Coskun AK, Jawanda N, Auer J, Sutton RE. Differential interaction between human and murine Crm1 and lentiviral Rev proteins. Virology 2018; 513:1-10. [PMID: 29028476 PMCID: PMC5914484 DOI: 10.1016/j.virol.2017.09.027] [Citation(s) in RCA: 6] [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: 06/05/2017] [Revised: 09/30/2017] [Accepted: 09/30/2017] [Indexed: 01/30/2023]
Abstract
Mice have multiple obstacles to HIV replication, including a block of unspliced and partially spliced viral mRNA nuclear export. In human, Rev binds to the Rev-response element and human (h) Crm1, facilitating nuclear export of RRE-containing viral RNAs. Murine (m) Crm1 is less functional than hCrm1 in this regard. Here we demonstrated that in biochemical experiments mCrm1 failed to interact with HIV Rev whereas hCrm1 did. In genetic experiments in human cells, we observed a modest but significant differential effect between mCrm1 and hCrm1, which was also true of other lentiviral Revs tested. Triple mutant hCrm1 P411T-M412V-F414S behaved similarly to mCrm1, whereas mCrm1 with T411P-V412M-S414F regained some activity, although contribution of additional residues to its function can not be excluded. Similar results were observed in murine cells. This suggests a differential interaction between hCrm1 and mCrm1 and many lentiviral Revs, which may partially explain the HIV replicative defect in mice.
Collapse
Affiliation(s)
- Yan Yue
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, United States
| | - Ayse K Coskun
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, United States
| | - Navneet Jawanda
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, United States
| | - Jim Auer
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, United States
| | - Richard E Sutton
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, United States.
| |
Collapse
|
16
|
Contributions of Individual Domains to Function of the HIV-1 Rev Response Element. J Virol 2017; 91:JVI.00746-17. [PMID: 28814520 DOI: 10.1128/jvi.00746-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 08/09/2017] [Indexed: 11/20/2022] Open
Abstract
The HIV-1 Rev response element (RRE) is a 351-base element in unspliced and partially spliced viral RNA; binding of the RRE by the viral Rev protein induces nuclear export of RRE-containing RNAs, as required for virus replication. It contains one long, imperfect double helix (domain I), one branched domain (domain II) containing a high-affinity Rev-binding site, and two or three additional domains. We previously reported that the RRE assumes an "A" shape in solution and suggested that the location of the Rev binding sites in domains I and II, opposite each other on the two legs of the A, is optimal for Rev binding and explains Rev's specificity for RRE-containing RNAs. Using small-angle X-ray scattering (SAXS) and a quantitative functional assay, we have now analyzed a panel of RRE mutants. All the results support the essential role of the A shape for RRE function. Moreover, they suggest that the distal portion of domain I and the three crowning domains all contribute to the maintenance of the A shape. Domains I and II are necessary and sufficient for substantial RRE function, provided they are joined by a flexible linker that allows the two domains to face each other.IMPORTANCE Retroviral replication requires that some of the viral RNAs transcribed in the cell nucleus be exported to the cytoplasm without being spliced. To achieve this, HIV-1 encodes a protein, Rev, which binds to a complex, highly structured element within viral RNA, the Rev response element (RRE), and escorts RRE-containing RNAs from the nucleus. We previously reported that the RRE is "A" shaped and suggested that this architecture, with the 2 legs opposite one another, can explain the specificity of Rev for the RRE. We have analyzed the functional contributions of individual RRE domains and now report that several domains contribute, with some redundancy, to maintenance of the overall RRE shape. The data strongly support the hypothesis that the opposed placement of the 2 legs is essential for RRE function.
Collapse
|
17
|
Schröder HC, Ushijima H, Bek A, Merz H, Pfeifer K, Müller WEG. Inhibition of Formation of Rev-RRE Complex by Pyronin Y. ACTA ACUST UNITED AC 2016. [DOI: 10.1177/095632029300400205] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The interaction of pyronin Y, an RNA intercalating drug, with the binding of Rev protein from human immunodeficiency virus type 1 (HIV-1) to Rev-responsive element (RRE)-containing env RNA was studied. In gel retardation assays, recombinant Rev protein tightly bound to in vitro transcribed RRE RNA. Nitrocellulose-filter-binding studies revealed a dissociation constant of ≈(1–2) = 10−10M (Pfeifer et al., 1991). Pyronin Y efficiently suppressed formation of the Rev-RRE complex. At a concentration of 1 μg ml−1, complex formation was almost completely inhibited. Electron microscopy showed that Rev oligomerizes in the presence of RRE-containing RNA with the formation of short rod-like structures or long filaments, depending on the length of the transcript. Assembly of Rev protein along RRE-containing RNAs was abolished after addition of pyronin Y. Thus pyronin Y represents the first compound described to inhibit Rev-RRE complex formation.
Collapse
Affiliation(s)
- H. C. Schröder
- Institut für Physiologische Chemie, Universität, Duesbergweg 6, 6500 Mainz, Germany
| | - H. Ushijima
- AIDS Research Center, National Institute of Health, Gakuen 4-7-1, Musashimurayama-shi, Tokyo 208, Japan
| | - A. Bek
- Institut für Physiologische Chemie, Universität, Duesbergweg 6, 6500 Mainz, Germany
| | - H. Merz
- Institut für Physiologische Chemie, Universität, Duesbergweg 6, 6500 Mainz, Germany
| | - K. Pfeifer
- Institut für Physiologische Chemie, Universität, Duesbergweg 6, 6500 Mainz, Germany
| | - W. E. G. Müller
- Institut für Physiologische Chemie, Universität, Duesbergweg 6, 6500 Mainz, Germany
| |
Collapse
|
18
|
Wynn JE, Zhang W, Tebit DM, Gray LR, Hammarskjold ML, Rekosh D, Santos WL. Effect of intercalator and Lewis acid-base branched peptide complex formation: boosting affinity towards HIV-1 RRE RNA. MEDCHEMCOMM 2016; 7:1436-1440. [PMID: 27453773 DOI: 10.1039/c6md00171h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
High throughput screening of a 4096 compound library of boronic acid and acridine containing branched peptides revealed compounds that have dissociation constants in the low nanomolar regime for HIV-1 RRE IIB RNA. We demonstrate that branched peptide boronic acids A5, A6, and A7 inhibit the production of p24, an HIV-1 capsid protein, in a dose-dependent manner.
Collapse
Affiliation(s)
- Jessica E Wynn
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24060, USA
| | - Wenyu Zhang
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24060, USA
| | - Denis M Tebit
- Department of Microbiology, Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, VA 22904, USA
| | - Laurie R Gray
- Department of Microbiology, Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, VA 22904, USA
| | - Marie-Louise Hammarskjold
- Department of Microbiology, Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, VA 22904, USA
| | - David Rekosh
- Department of Microbiology, Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, VA 22904, USA
| | - Webster L Santos
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24060, USA
| |
Collapse
|
19
|
DiMattia MA, Watts NR, Cheng N, Huang R, Heymann JB, Grimes JM, Wingfield PT, Stuart DI, Steven AC. The Structure of HIV-1 Rev Filaments Suggests a Bilateral Model for Rev-RRE Assembly. Structure 2016; 24:1068-80. [PMID: 27265851 DOI: 10.1016/j.str.2016.04.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 04/21/2016] [Accepted: 04/25/2016] [Indexed: 11/24/2022]
Abstract
HIV-1 Rev protein mediates the nuclear export of viral RNA genomes. To do so, Rev oligomerizes cooperatively onto an RNA motif, the Rev response element (RRE), forming a complex that engages with the host nuclear export machinery. To better understand Rev oligomerization, we determined four crystal structures of Rev N-terminal domain dimers, which show that they can pivot about their dyad axis, giving crossing angles of 90° to 140°. In parallel, we performed cryoelectron microscopy of helical Rev filaments. Filaments vary from 11 to 15 nm in width, reflecting variations in dimer crossing angle. These structures contain additional density, indicating that C-terminal domains become partially ordered in the context of filaments. This conformational variability may be exploited in the assembly of RRE/Rev complexes. Our data also revealed a third interface between Revs, which offers an explanation for how the arrangement of Rev subunits adapts to the "A"-shaped architecture of the RRE in export-active complexes.
Collapse
Affiliation(s)
- Michael A DiMattia
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Headington OX3 7BN, UK
| | - Norman R Watts
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Naiqian Cheng
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rick Huang
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - J Bernard Heymann
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jonathan M Grimes
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Headington OX3 7BN, UK; Diamond House, Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Paul T Wingfield
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - David I Stuart
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Headington OX3 7BN, UK; Diamond House, Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Alasdair C Steven
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|
20
|
Weinreb C, Riesselman AJ, Ingraham JB, Gross T, Sander C, Marks DS. 3D RNA and Functional Interactions from Evolutionary Couplings. Cell 2016; 165:963-75. [PMID: 27087444 DOI: 10.1016/j.cell.2016.03.030] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 01/15/2016] [Accepted: 03/18/2016] [Indexed: 11/18/2022]
Abstract
Non-coding RNAs are ubiquitous, but the discovery of new RNA gene sequences far outpaces the research on the structure and functional interactions of these RNA gene sequences. We mine the evolutionary sequence record to derive precise information about the function and structure of RNAs and RNA-protein complexes. As in protein structure prediction, we use maximum entropy global probability models of sequence co-variation to infer evolutionarily constrained nucleotide-nucleotide interactions within RNA molecules and nucleotide-amino acid interactions in RNA-protein complexes. The predicted contacts allow all-atom blinded 3D structure prediction at good accuracy for several known RNA structures and RNA-protein complexes. For unknown structures, we predict contacts in 160 non-coding RNA families. Beyond 3D structure prediction, evolutionary couplings help identify important functional interactions-e.g., at switch points in riboswitches and at a complex nucleation site in HIV. Aided by increasing sequence accumulation, evolutionary coupling analysis can accelerate the discovery of functional interactions and 3D structures involving RNA.
Collapse
Affiliation(s)
- Caleb Weinreb
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Adam J Riesselman
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Program in Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - John B Ingraham
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Torsten Gross
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Institute of Pathology, Charité - Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Chris Sander
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Debora S Marks
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
21
|
Fernandes JD, Booth DS, Frankel AD. A structurally plastic ribonucleoprotein complex mediates post-transcriptional gene regulation in HIV-1. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:470-86. [PMID: 26929078 DOI: 10.1002/wrna.1342] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 01/12/2016] [Accepted: 01/14/2016] [Indexed: 01/28/2023]
Abstract
HIV replication requires the nuclear export of essential, intron-containing viral RNAs. To facilitate export, HIV encodes the viral accessory protein Rev which binds unspliced and partially spliced viral RNAs and creates a ribonucleoprotein complex that recruits the cellular Chromosome maintenance factor 1 export machinery. Exporting RNAs in this manner bypasses the necessity for complete splicing as a prerequisite for mRNA export, and allows intron-containing RNAs to reach the cytoplasm intact for translation and virus packaging. Recent structural studies have revealed that this entire complex exhibits remarkable plasticity at many levels of organization, including RNA folding, protein-RNA recognition, multimer formation, and host factor recruitment. In this review, we explore each aspect of plasticity from structural, functional, and possible therapeutic viewpoints. WIREs RNA 2016, 7:470-486. doi: 10.1002/wrna.1342 For further resources related to this article, please visit the WIREs website.
Collapse
Affiliation(s)
- Jason D Fernandes
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - David S Booth
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Alan D Frankel
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| |
Collapse
|
22
|
Lichinchi G, Gao S, Saletore Y, Gonzalez GM, Bansal V, Wang Y, Mason CE, Rana TM. Dynamics of the human and viral m(6)A RNA methylomes during HIV-1 infection of T cells. Nat Microbiol 2016; 1:16011. [PMID: 27572442 DOI: 10.1038/nmicrobiol.2016.11] [Citation(s) in RCA: 321] [Impact Index Per Article: 40.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 01/22/2016] [Indexed: 12/22/2022]
Abstract
N(6)-methyladenosine (m(6)A) is the most prevalent internal modification of eukaryotic mRNA. Very little is known of the function of m(6)A in the immune system or its role in host-pathogen interactions. Here, we investigate the topology, dynamics and bidirectional influences of the viral-host RNA methylomes during HIV-1 infection of human CD4 T cells. We show that viral infection triggers a massive increase in m(6)A in both host and viral mRNAs. In HIV-1 mRNA, we identified 14 methylation peaks in coding and noncoding regions, splicing junctions and splicing regulatory sequences. We also identified a set of 56 human gene transcripts that were uniquely methylated in HIV-1-infected T cells and were enriched for functions in viral gene expression. The functional relevance of m(6)A for viral replication was demonstrated by silencing of the m(6)A writer or the eraser enzymes, which decreased or increased HIV-1 replication, respectively. Furthermore, methylation of two conserved adenosines in the stem loop II region of HIV-1 Rev response element (RRE) RNA enhanced binding of HIV-1 Rev protein to the RRE in vivo and influenced nuclear export of RNA. Our results identify a new mechanism for the control of HIV-1 replication and its interaction with the host immune system.
Collapse
Affiliation(s)
- Gianluigi Lichinchi
- Department of Pediatrics, University of California, San Diego School of Medicine, La Jolla, California 92093, USA.,Program for RNA Biology and Graduate School of Biomedical Sciences, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Shang Gao
- Department of Pediatrics, University of California, San Diego School of Medicine, La Jolla, California 92093, USA
| | - Yogesh Saletore
- Department of Physiology and Biophysics and the Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University, 1305 York Avenue, New York, New York 10021, USA
| | - Gwendolyn Michelle Gonzalez
- Environmental Toxicology Graduate Program and Department of Chemistry, University of California, Riverside, California 92521, USA
| | - Vikas Bansal
- Department of Pediatrics, University of California, San Diego School of Medicine, La Jolla, California 92093, USA
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program and Department of Chemistry, University of California, Riverside, California 92521, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics and the Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University, 1305 York Avenue, New York, New York 10021, USA.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, The Feil Family Brain and Mind Research Institute (BMRI), New York, New York, 10021, USA
| | - Tariq M Rana
- Department of Pediatrics, University of California, San Diego School of Medicine, La Jolla, California 92093, USA.,Program for RNA Biology and Graduate School of Biomedical Sciences, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA.,Institute for Genomic Medicine and Moores Cancer Center, University of California San Diego, La Jolla, California 92093, USA
| |
Collapse
|
23
|
Tanamura S, Terakado H, Harada K. Cooperative dimerization of a stably folded protein directed by a flexible RNA in the assembly of the HIV Rev dimer-RRE stem II complex. J Mol Recognit 2015; 29:199-209. [PMID: 26620599 DOI: 10.1002/jmr.2518] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 10/13/2015] [Accepted: 10/17/2015] [Indexed: 11/08/2022]
Abstract
The binding of the HIV-1 Rev protein as an oligomer to a viral RNA element, the Rev-response element (RRE), mediates nuclear export of genomic RNA. Assembly of the Rev-RRE ribonucleoprotein (RNP) complex is nucleated by the binding of the first Rev molecule to stem IIB of the RRE. This is followed by stepwise addition of a total of ~six Rev molecules along the RRE through a combination of RNA-protein and protein-protein interactions. RRE stem II, which forms a three-way junction consisting of stems IIA, IIB and IIC, has been shown to bind to two Rev molecules in a cooperative manner, with the second Rev molecule binding to the junction region of stem II. The results of base substitutions at the stem II junction, and characterization of stem II junction variants selected from a randomized library showed that an "open" flexible structure is preferred for binding of the second Rev molecule, and that binding of the second Rev molecule to the junction region is not sequence-specific. Alanine substitutions of a number of Rev amino acid residues implicated to be important for Rev folding in previous structural studies were found to result in a dramatic decrease in the binding of the second Rev molecule. These results support the model that proper folding of Rev is critical in ensuring that the flexible RRE is able to correctly position Rev molecules for specific RNP assembly, and suggests that targeting Rev folding may be effective in the inhibition of Rev function.
Collapse
Affiliation(s)
- Satoshi Tanamura
- Department of Life Sciences, Tokyo Gakugei University, Koganei, Tokyo, 184-8501, Japan
| | - Hiroto Terakado
- Department of Life Sciences, Tokyo Gakugei University, Koganei, Tokyo, 184-8501, Japan
| | - Kazuo Harada
- Department of Life Sciences, Tokyo Gakugei University, Koganei, Tokyo, 184-8501, Japan
| |
Collapse
|
24
|
HIV Rev Assembly on the Rev Response Element (RRE): A Structural Perspective. Viruses 2015; 7:3053-75. [PMID: 26075509 PMCID: PMC4488727 DOI: 10.3390/v7062760] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 06/05/2015] [Indexed: 01/18/2023] Open
Abstract
HIV-1 Rev is an ~13 kD accessory protein expressed during the early stage of virus replication. After translation, Rev enters the nucleus and binds the Rev response element (RRE), a ~350 nucleotide, highly structured element embedded in the env gene in unspliced and singly spliced viral RNA transcripts. Rev-RNA assemblies subsequently recruit Crm1 and other cellular proteins to form larger complexes that are exported from the nucleus. Once in the cytoplasm, the complexes dissociate and unspliced and singly-spliced viral RNAs are packaged into nascent virions or translated into viral structural proteins and enzymes, respectively. Rev binding to the RRE is a complex process, as multiple copies of the protein assemble on the RNA in a coordinated fashion via a series of Rev-Rev and Rev-RNA interactions. Our understanding of the nature of these interactions has been greatly advanced by recent studies using X-ray crystallography, small angle X-ray scattering (SAXS) and single particle electron microscopy as well as biochemical and genetic methodologies. These advances are discussed in detail in this review, along with perspectives on development of antiviral therapies targeting the HIV-1 RRE.
Collapse
|
25
|
Sherpa C, Rausch JW, Le Grice SFJ, Hammarskjold ML, Rekosh D. The HIV-1 Rev response element (RRE) adopts alternative conformations that promote different rates of virus replication. Nucleic Acids Res 2015; 43:4676-86. [PMID: 25855816 PMCID: PMC4482075 DOI: 10.1093/nar/gkv313] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/27/2015] [Indexed: 01/03/2023] Open
Abstract
The HIV Rev protein forms a complex with a 351 nucleotide sequence present in unspliced and incompletely spliced human immunodeficiency virus (HIV) mRNAs, the Rev response element (RRE), to recruit the cellular nuclear export receptor Crm1 and Ran-GTP. This complex facilitates nucleo-cytoplasmic export of these mRNAs. The precise secondary structure of the HIV-1 RRE has been controversial, since studies have reported alternative structures comprising either four or five stem-loops. The published structures differ only in regions that lie outside of the primary Rev binding site. Using in-gel SHAPE, we have now determined that the wt NL4-3 RRE exists as a mixture of both structures. To assess functional differences between these RRE ‘conformers’, we created conformationally locked mutants by site-directed mutagenesis. Using subgenomic reporters, as well as HIV replication assays, we demonstrate that the five stem-loop form of the RRE promotes greater functional Rev/RRE activity compared to the four stem-loop counterpart.
Collapse
Affiliation(s)
- Chringma Sherpa
- Myles H. Thaler Center for AIDS and Human Retrovirus Research, Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA 22908, USA
| | - Jason W Rausch
- Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD 21702, USA
| | - Stuart F J Le Grice
- Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD 21702, USA
| | - Marie-Louise Hammarskjold
- Myles H. Thaler Center for AIDS and Human Retrovirus Research, Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA 22908, USA
| | - David Rekosh
- Myles H. Thaler Center for AIDS and Human Retrovirus Research, Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA 22908, USA
| |
Collapse
|
26
|
Small-angle X-ray scattering: a bridge between RNA secondary structures and three-dimensional topological structures. Curr Opin Struct Biol 2015; 30:147-160. [PMID: 25765781 DOI: 10.1016/j.sbi.2015.02.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 02/17/2015] [Accepted: 02/18/2015] [Indexed: 11/20/2022]
Abstract
Whereas the structures of small to medium-sized well folded RNA molecules often can be determined by either X-ray crystallography or NMR spectroscopy, obtaining structural information for large RNAs using experimental, computational, or combined approaches remains a major interest and challenge. RNA is very sensitive to small-angle X-ray scattering (SAXS) due to high electron density along phosphate-sugar backbones, whose scattering contribution dominates SAXS intensity. For this reason, SAXS is particularly useful in obtaining global RNA structural information that outlines backbone topologies and, therefore, molecular envelopes. Such information is extremely valuable in bridging the gap between the secondary structures and three-dimensional topological structures of RNA molecules, particularly those that have proven difficult to study using other structure-determination methods. Here we review published results of RNA topological structures derived from SAXS data or in combination with other experimental data, as well as details on RNA sample preparation for SAXS experiments.
Collapse
|
27
|
Jayaraman B, Crosby DC, Homer C, Ribeiro I, Mavor D, Frankel AD. RNA-directed remodeling of the HIV-1 protein Rev orchestrates assembly of the Rev-Rev response element complex. eLife 2014; 3:e04120. [PMID: 25486594 PMCID: PMC4360532 DOI: 10.7554/elife.04120] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 12/06/2014] [Indexed: 12/27/2022] Open
Abstract
The HIV-1 protein Rev controls a critical step in viral replication by mediating the nuclear export of unspliced and singly-spliced viral mRNAs. Multiple Rev subunits assemble on the Rev Response Element (RRE), a structured region present in these RNAs, and direct their export through the Crm1 pathway. Rev-RRE assembly occurs via several Rev oligomerization and RNA-binding steps, but how these steps are coordinated to form an export-competent complex is unclear. Here, we report the first crystal structure of a Rev dimer-RRE complex, revealing a dramatic rearrangement of the Rev-dimer upon RRE binding through re-packing of its hydrophobic protein-protein interface. Rev-RNA recognition relies on sequence-specific contacts at the well-characterized IIB site and local RNA architecture at the second site. The structure supports a model in which the RRE utilizes the inherent plasticity of Rev subunit interfaces to guide the formation of a functional complex.
Collapse
MESH Headings
- Active Transport, Cell Nucleus
- Binding Sites
- Cell Line, Tumor
- Cell Nucleus/metabolism
- Cell Nucleus/virology
- Crystallography, X-Ray
- Cytosol/metabolism
- Cytosol/virology
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression Regulation
- HEK293 Cells
- HIV-1/genetics
- HIV-1/metabolism
- HeLa Cells
- Host-Pathogen Interactions
- Humans
- Karyopherins/genetics
- Karyopherins/metabolism
- Models, Molecular
- Protein Binding
- RNA Splicing
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Receptors, Cytoplasmic and Nuclear/genetics
- Receptors, Cytoplasmic and Nuclear/metabolism
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Response Elements
- Signal Transduction
- T-Lymphocytes/metabolism
- T-Lymphocytes/virology
- Virus Replication/genetics
- rev Gene Products, Human Immunodeficiency Virus/chemistry
- rev Gene Products, Human Immunodeficiency Virus/genetics
- rev Gene Products, Human Immunodeficiency Virus/metabolism
- Exportin 1 Protein
Collapse
Affiliation(s)
- Bhargavi Jayaraman
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - David C Crosby
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Christina Homer
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Isabel Ribeiro
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - David Mavor
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Alan D Frankel
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| |
Collapse
|
28
|
Bai Y, Tambe A, Zhou K, Doudna JA. RNA-guided assembly of Rev-RRE nuclear export complexes. eLife 2014; 3:e03656. [PMID: 25163983 PMCID: PMC4142337 DOI: 10.7554/elife.03656] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 08/05/2014] [Indexed: 11/13/2022] Open
Abstract
HIV replication requires nuclear export of unspliced and singly spliced viral transcripts. Although a unique RNA structure has been proposed for the Rev-response element (RRE) responsible for viral mRNA export, how it recruits multiple HIV Rev proteins to form an export complex has been unclear. We show here that initial binding of Rev to the RRE triggers RNA tertiary structural changes, enabling further Rev binding and the rapid formation of a viral export complex. Analysis of the Rev-RRE assembly pathway using SHAPE-Seq and small-angle X-ray scattering (SAXS) reveals two major steps of Rev-RRE complex formation, beginning with rapid Rev binding to a pre-organized region presenting multiple Rev binding sites. This step induces long-range remodeling of the RNA to expose a cryptic Rev binding site, enabling rapid assembly of additional Rev proteins into the RNA export complex. This kinetic pathway may help maintain the balance between viral replication and maturation.DOI: http://dx.doi.org/10.7554/eLife.03656.001.
Collapse
Affiliation(s)
- Yun Bai
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Akshay Tambe
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Kaihong Zhou
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States Department of Chemistry, University of California, Berkeley, Berkeley, United States Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| |
Collapse
|
29
|
Fang X, Wang J, O’Carroll IP, Mitchell M, Zuo X, Wang Y, Yu P, Liu Y, Rausch JW, Dyba MA, Kjems J, Schwieters CD, Seifert S, Winans RE, Watts NR, Stahl SJ, Wingfield PT, Byrd RA, Le Grice SF, Rein A, Wang YX. An unusual topological structure of the HIV-1 Rev response element. Cell 2013; 155:594-605. [PMID: 24243017 PMCID: PMC3918456 DOI: 10.1016/j.cell.2013.10.008] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 08/22/2013] [Accepted: 10/07/2013] [Indexed: 01/15/2023]
Abstract
Nuclear export of unspliced and singly spliced viral mRNA is a critical step in the HIV life cycle. The structural basis by which the virus selects its own mRNA among more abundant host cellular RNAs for export has been a mystery for more than 25 years. Here, we describe an unusual topological structure that the virus uses to recognize its own mRNA. The viral Rev response element (RRE) adopts an "A"-like structure in which the two legs constitute two tracks of binding sites for the viral Rev protein and position the two primary known Rev-binding sites ~55 Å apart, matching the distance between the two RNA-binding motifs in the Rev dimer. Both the legs of the "A" and the separation between them are required for optimal RRE function. This structure accounts for the specificity of Rev for the RRE and thus the specific recognition of the viral RNA.
Collapse
MESH Headings
- Active Transport, Cell Nucleus
- Base Sequence
- Binding Sites
- Cell Nucleus/metabolism
- HEK293 Cells
- HIV-1/chemistry
- HIV-1/genetics
- Humans
- Molecular Sequence Data
- Nuclear Pore/metabolism
- Nucleic Acid Conformation
- RNA Folding
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Scattering, Small Angle
- X-Ray Diffraction
- rev Gene Products, Human Immunodeficiency Virus/chemistry
- rev Gene Products, Human Immunodeficiency Virus/genetics
- rev Gene Products, Human Immunodeficiency Virus/metabolism
Collapse
Affiliation(s)
- Xianyang Fang
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Jinbu Wang
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Ina P. O’Carroll
- Retroviral Assembly Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Michelle Mitchell
- RT Biochemistry Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Xiaobing Zuo
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Yi Wang
- RT Biochemistry Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Ping Yu
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
- Structural Biophysics Laboratory, SAIC-Frederick, Frederick, MD 21702, USA
| | - Yu Liu
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Jason W. Rausch
- RT Biochemistry Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Marzena A. Dyba
- Structural Biophysics Laboratory, SAIC-Frederick, Frederick, MD 21702, USA
| | - Jørgen Kjems
- Department of Molecular Biology, University of Aarhus, DK-8000 Aarhus C, Denmark
| | - Charles D. Schwieters
- Division of Computational Bioscience, Center for Informational Technology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Soenke Seifert
- X-ray Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Randall E. Winans
- X-ray Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
| | - Norman R. Watts
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephen J. Stahl
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul T. Wingfield
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - R. Andrew Byrd
- Macromolecular NMR Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Stuart F.J. Le Grice
- RT Biochemistry Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Alan Rein
- Retroviral Assembly Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| |
Collapse
|
30
|
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.
Collapse
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:
| |
Collapse
|
31
|
Delhalle S, Schmit JC, Chevigné A. Phages and HIV-1: from display to interplay. Int J Mol Sci 2012; 13:4727-4794. [PMID: 22606007 PMCID: PMC3344243 DOI: 10.3390/ijms13044727] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 03/26/2012] [Accepted: 03/30/2012] [Indexed: 11/16/2022] Open
Abstract
The complex hide-and-seek game between HIV-1 and the host immune system has impaired the development of an efficient vaccine. In addition, the high variability of the virus impedes the long-term control of viral replication by small antiviral drugs. For more than 20 years, phage display technology has been intensively used in the field of HIV-1 to explore the epitope landscape recognized by monoclonal and polyclonal HIV-1-specific antibodies, thereby providing precious data about immunodominant and neutralizing epitopes. In parallel, biopanning experiments with various combinatorial or antibody fragment libraries were conducted on viral targets as well as host receptors to identify HIV-1 inhibitors. Besides these applications, phage display technology has been applied to characterize the enzymatic specificity of the HIV-1 protease. Phage particles also represent valuable alternative carriers displaying various HIV-1 antigens to the immune system and eliciting antiviral responses. This review presents and summarizes the different studies conducted with regard to the nature of phage libraries, target display mode and biopanning procedures.
Collapse
Affiliation(s)
- Sylvie Delhalle
- Laboratory of Retrovirology, CRP-Sante, 84, Val Fleuri, L-1526 Luxembourg, Luxembourg; E-Mails: (J.-C.S.); (A.C.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +352-26970211; Fax: +352-26970221
| | - Jean-Claude Schmit
- Laboratory of Retrovirology, CRP-Sante, 84, Val Fleuri, L-1526 Luxembourg, Luxembourg; E-Mails: (J.-C.S.); (A.C.)
- Service National des Maladies Infectieuses, Centre Hospitalier Luxembourg, 4, rue E. Barblé, L-1210 Luxembourg, Luxembourg
| | - Andy Chevigné
- Laboratory of Retrovirology, CRP-Sante, 84, Val Fleuri, L-1526 Luxembourg, Luxembourg; E-Mails: (J.-C.S.); (A.C.)
| |
Collapse
|
32
|
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.
Collapse
|
33
|
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.
Collapse
Affiliation(s)
- Jason Fernandes
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | | | | |
Collapse
|
34
|
Chung J, Rossi JJ, Jung U. Current progress and challenges in HIV gene therapy. Future Virol 2011; 6:1319-1328. [PMID: 22754586 DOI: 10.2217/fvl.11.113] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
HIV-1 causes AIDS, a syndrome that affects millions of people globally. Existing HAART is efficient in slowing down disease progression but cannot eradicate the virus. Furthermore the severity of the side effects and the emergence of drug-resistant mutants call for better therapy. Gene therapy serves as an attractive alternative as it reconstitutes the immune system with HIV-resistant cells and could thereby provide a potential cure. The feasibility of this approach was first demonstrated with the 'Berlin patient', who was functionally cured from HIV/AIDS with undetectable HIV-1 viral load after transplantation of bone marrow harboring a naturally occurring CCR5 mutation that blocks viral entry. Here, we give an overview of the current status of HIV gene therapy and remaining challenges and obstacles.
Collapse
Affiliation(s)
- Janet Chung
- Division of Molecular & Cell Biology, Beckman Research Institute of the City of Hope, 1500 East Duarte Road, CA 91010, USA
| | | | | |
Collapse
|
35
|
Kumar S, Bose D, Suryawanshi H, Sabharwal H, Mapa K, Maiti S. Specificity of RSG-1.2 peptide binding to RRE-IIB RNA element of HIV-1 over Rev peptide is mainly enthalpic in origin. PLoS One 2011; 6:e23300. [PMID: 21853108 PMCID: PMC3154333 DOI: 10.1371/journal.pone.0023300] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Accepted: 07/12/2011] [Indexed: 02/03/2023] Open
Abstract
Rev is an essential HIV-1 regulatory protein which binds to the Rev responsive element (RRE) present within the env gene of HIV-1 RNA genome. This binding facilitates the transport of the RNA to the cytoplasm, which in turn triggers the switch between viral latency and active viral replication. Essential components of this complex have been localized to a minimal arginine rich Rev peptide and stem IIB region of RRE. A synthetic peptide known as RSG-1.2 binds with high binding affinity and specificity to the RRE-IIB than the Rev peptide, however the thermodynamic basis of this specificity has not yet been addressed. The present study aims to probe the thermodynamic origin of this specificity of RSG-1.2 over Rev Peptide for RRE-IIB. The temperature dependent melting studies show that RSG-1.2 binding stabilizes the RRE structure significantly (ΔTm = 4.3°C), in contrast to Rev binding. Interestingly the thermodynamic signatures of the binding have also been found to be different for both the peptides. At pH 7.5, RSG-1.2 binds RRE-IIB with a Ka = 16.2±0.6×107 M−1 where enthalpic change ΔH = −13.9±0.1 kcal/mol is the main driving force with limited unfavorable contribution from entropic change TΔS = −2.8±0.1 kcal/mol. A large part of ΔH may be due to specific stacking between U72 and Arg15. In contrast binding of Rev (Ka = 3.1±0.4×107 M−1) is driven mainly by entropy (ΔH = 0 kcal/mol and TΔS = 10.2±0.2 kcal/mol) which arises from major conformational changes in the RNA upon binding.
Collapse
Affiliation(s)
- Santosh Kumar
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Delhi, India
| | - Debojit Bose
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Delhi, India
| | - Hemant Suryawanshi
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Delhi, India
| | - Harshana Sabharwal
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Delhi, India
| | - Koyeli Mapa
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Delhi, India
| | - Souvik Maiti
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Delhi, India
- * E-mail:
| |
Collapse
|
36
|
Lee J, Choi H, Cho J, Lee DG. Effects of positively charged arginine residues on membrane pore forming activity of Rev-NIS peptide in bacterial cells. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:2421-7. [PMID: 21762675 DOI: 10.1016/j.bbamem.2011.06.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 06/23/2011] [Accepted: 06/27/2011] [Indexed: 11/19/2022]
Abstract
Here, we investigated antibacterial effects of Rev-NIS and suggested the role of positively charged amino acids on membrane pore forming activity of the peptide in bacterial cells, by synthesizing two analogs, Anal R and Anal S. Based on the amphipathic property of Rev-NIS, Anal R and Anal S were designed by substituting E(1) and L(3) to R and L(3) to S, respectively. The circular dichroism (CD) spectroscopy showed that Anal R and Anal S have the same conformation of Rev-NIS, with a significant fraction of helical structure. In succession, the antibacterial susceptibility testing showed that Rev-NIS and its analogs possessed significant activities (Anal R>Rev-NIS>Anal S), without hemolytic effects, against bacterial pathogens including antibiotics-resistant strains. Moreover, the membrane studies, 3,3'-dipropylthiadicarbocyanine iodide (diSC(3)5) staining and FITC-dextran (FD) leakage assay demonstrated that the analogs as well as Rev-NIS acted on the bacterial membranes and potently made pores, with the hydrodynamic radius between 1.4nm and 2.3nm. Especially, Anal R made larger pores than other peptides, with the radius between 2.3nm and 3.3nm. These results also corresponded to the result of antibacterial susceptibility testing. In summary, this study indicates that the two arginine residues are more influential than the hydrophobicity or the helicity, regarding the molecular activity of the peptide, and finally suggests that Anal R peptide may be applied to novel antibacterial agents.
Collapse
Affiliation(s)
- Juneyoung Lee
- Kyungpook National University, Daegu, Republic of Korea
| | | | | | | |
Collapse
|
37
|
Siman P, Blatt O, Moyal T, Danieli T, Lebendiker M, Lashuel HA, Friedler A, Brik A. Chemical Synthesis and Expression of the HIV-1 Rev Protein. Chembiochem 2011; 12:1097-104. [DOI: 10.1002/cbic.201100033] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Indexed: 01/20/2023]
|
38
|
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.
Collapse
Affiliation(s)
- Thomas Vercruysse
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Daugherty MD, Liu B, Frankel AD. Structural basis for cooperative RNA binding and export complex assembly by HIV Rev. Nat Struct Mol Biol 2010; 17:1337-42. [PMID: 20953181 PMCID: PMC2988976 DOI: 10.1038/nsmb.1902] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Accepted: 08/06/2010] [Indexed: 12/28/2022]
Abstract
HIV replication requires nuclear export of unspliced viral RNAs to translate structural proteins and package genomic RNA. Export is mediated by cooperative binding of the Rev protein to the Rev response element (RRE) RNA, to form a highly specific oligomeric ribonucleoprotein (RNP) that binds to the Crm1 host export factor. To understand how protein oligomerization generates cooperativity and specificity for RRE binding, we solved the crystal structure of a Rev dimer at 2.5-Å resolution. The dimer arrangement organizes arginine-rich helices at the ends of a V-shaped assembly to bind adjacent RNA sites and structurally couple dimerization and RNA recognition. A second protein-protein interface arranges higher-order Rev oligomers to act as an adaptor to the host export machinery, with viral RNA bound to one face and Crm1 to another, the oligomers thereby using small, interconnected modules to physically arrange the RNP for efficient export.
Collapse
MESH Headings
- Amino Acid Sequence
- Binding Sites
- Conserved Sequence
- Crystallography, X-Ray
- Dimerization
- HIV-1/physiology
- Karyopherins/metabolism
- Models, Molecular
- Molecular Sequence Data
- Protein Structure, Tertiary
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Receptors, Cytoplasmic and Nuclear/metabolism
- Response Elements
- Sequence Alignment
- Virus Replication
- rev Gene Products, Human Immunodeficiency Virus/chemistry
- rev Gene Products, Human Immunodeficiency Virus/metabolism
- rev Gene Products, Human Immunodeficiency Virus/physiology
- Exportin 1 Protein
Collapse
Affiliation(s)
- Matthew D. Daugherty
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco San Francisco, CA 94158
| | - Bella Liu
- Department of Biochemistry and Biophysics, University of California, San Francisco San Francisco, CA 94158
| | - Alan D. Frankel
- Department of Biochemistry and Biophysics, University of California, San Francisco San Francisco, CA 94158
| |
Collapse
|
40
|
HIV Rev response element (RRE) directs assembly of the Rev homooligomer into discrete asymmetric complexes. Proc Natl Acad Sci U S A 2010; 107:12481-6. [PMID: 20616058 DOI: 10.1073/pnas.1007022107] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
RNA is a crucial structural component of many ribonucleoprotein (RNP) complexes, including the ribosome, spliceosome, and signal recognition particle, but the role of RNA in guiding complex formation is only beginning to be explored. In the case of HIV, viral replication requires assembly of an RNP composed of the Rev protein homooligomer and the Rev response element (RRE) RNA to mediate nuclear export of unspliced viral mRNAs. Assembly of the functional Rev-RRE complex proceeds by cooperative oligomerization of Rev on the RRE scaffold and utilizes both protein-protein and protein-RNA interactions to organize complexes with high specificity. The structures of the Rev protein and a peptide-RNA complex are known, but the complete RNP is not, making it unclear to what extent RNA defines the composition and architecture of Rev-RNA complexes. Here we show that the RRE controls the oligomeric state and solubility of Rev and guides its assembly into discrete Rev-RNA complexes. SAXS and EM data were used to derive a structural model of a Rev dimer bound to an essential RRE hairpin and to visualize the complete Rev-RRE RNP, demonstrating that RRE binding drives assembly of Rev homooligomers into asymmetric particles, reminiscent of the role of RNA in organizing more complex RNP machines, such as the ribosome, composed of many different protein subunits. Thus, the RRE is not simply a passive scaffold onto which proteins bind but instead actively defines the protein composition and organization of the RNP.
Collapse
|
41
|
Michael LA, Chenault JA, Miller BR, Knolhoff AM, Nagan MC. Water, Shape Recognition, Salt Bridges, and Cation–Pi Interactions Differentiate Peptide Recognition of the HIV Rev-Responsive Element. J Mol Biol 2009; 392:774-86. [DOI: 10.1016/j.jmb.2009.07.047] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2009] [Revised: 07/06/2009] [Accepted: 07/16/2009] [Indexed: 10/20/2022]
|
42
|
Sugaya M, Nishino N, Katoh A, Harada K. Amino acid requirement for the high affinity binding of a selected arginine-rich peptide with the HIV Rev-response element RNA. J Pept Sci 2008; 14:924-35. [PMID: 18351707 DOI: 10.1002/psc.1027] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The arginine-rich motif is a class of short arginine-rich peptides that bind to specific RNA structures that has been found to be a versatile framework for the design and selection of RNA-binding peptides. We previously identified novel peptides that bind to the Rev-response element (RRE) RNA of the HIV from an arginine-rich polypeptide library (ARPL) consisting of a polyarginine (15 mer) randomized at the N-terminal 10 positions. The selected peptides bound more strongly to the RRE than the natural binding partner, Rev, and contained glutamine residues that were assumed to be important for recognition of the G-A base pair. In addition, the peptides were predicted to bind to the RRE in an alpha-helical conformation. In this study, in order to understand the mechanism of the interaction between the RRE and the putative alpha-helical glutamine-containing peptides, the amino acid requirements for high affinity binding were analyzed by a combinatorial approach using a bacterial system for detecting RNA-peptide interactions. A consensus peptide, the DLA peptide, was elucidated, which consists of a single glutamine residue within a polyarginine context with the glutamine residue flanked at specific positions by three nonarginine residues, two of which appear to be important for alpha-helix stabilization. In addition, the DLA peptide was found to bind extremely tightly to the RRE with an affinity 50-fold higher than that of the Rev peptide as determined by a gel shift assay. A working model for the interaction of the DLA peptide to the RRE is proposed, which should aid in the development of peptide-based drugs that inhibit HIV replication, as well as in our understanding of polypeptide-RNA interactions.
Collapse
Affiliation(s)
- Maki Sugaya
- Department of Materials and Life Science, Faculty of Science and Technology, Seikei University, Musashino, Tokyo 180-8633, Japan
| | | | | | | |
Collapse
|
43
|
Daugherty MD, D'Orso I, Frankel AD. A solution to limited genomic capacity: using adaptable binding surfaces to assemble the functional HIV Rev oligomer on RNA. Mol Cell 2008; 31:824-34. [PMID: 18922466 DOI: 10.1016/j.molcel.2008.07.016] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2008] [Revised: 06/10/2008] [Accepted: 07/01/2008] [Indexed: 11/30/2022]
Abstract
Many ribonucleoprotein (RNP) complexes assemble into large, organized structures in which protein subunits are positioned by interactions with RNA and other proteins. Here we demonstrate that HIV Rev, constrained in size by a limited viral genome, also forms an organized RNP by assembling a homo-oligomer on the Rev response element (RRE) RNA. Rev subunits bind cooperatively to discrete RNA sites using an oligomerization domain and an adaptable protein-RNA interface, forming a complex with 500-fold higher affinity than the tightest single interaction. High-affinity binding correlates strongly with RNA export activity. Rev utilizes different surfaces of its alpha-helical RNA-binding domain to recognize several low-affinity binding sites, including the well-characterized stem IIB site and an additional site in stem IA. We propose that adaptable RNA-binding surfaces allow the Rev oligomer to assemble economically into a discrete, stable RNP and provide a mechanistic role for Rev oligomerization during the HIV life cycle.
Collapse
Affiliation(s)
- Matthew D Daugherty
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, CA 94158, USA
| | | | | |
Collapse
|
44
|
Savvateeva-Popova E, Medvedeva A, Popov A, Evgen'ev M. Role of non-coding RNAs in neurodegeneration and stress response in Drosophila. Biotechnol J 2008; 3:1010-21. [PMID: 18702036 DOI: 10.1002/biot.200800120] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The inherent limitations of genetic analysis in humans and other mammals as well as striking conservation of most genes controlling nervous system functioning in flies and mammals made Drosophila an attractive model to investigate various aspects of brain diseases. Since RNA research has made great progress in recent years here we present an overview of studies demonstrating the role of various non-coding RNAs in neurodegeneration and stress response in Drosophila as a model organism. We put special emphasis on the role of non-coding micro RNAs, hsr-omega transcripts, and artificial small highly structured RNAs as triggers of neuropathology including aggregates formation, cognitive abnormalities and other symptoms. Cellular stress is a conspicuous feature of many neurodegenerative diseases and the production of specialized proteins protects the nerve cells against aggregates formation. Therefore, herein we describe some data implicating various classes of non-coding RNAs in stress response in Drosophila. All these findings highlight Drosophila as an important model system to investigate various brain diseases potentially mediated by some non-coding RNAs including polyglutamine diseases, Alzheimer's disease, Huntigton's disease, and many others.
Collapse
|
45
|
Marenchino M, Armbruster DW, Hennig M. Rapid and efficient purification of RNA-binding proteins: application to HIV-1 Rev. Protein Expr Purif 2008; 63:112-9. [PMID: 18852051 DOI: 10.1016/j.pep.2008.09.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Revised: 09/04/2008] [Accepted: 09/10/2008] [Indexed: 10/21/2022]
Abstract
Non-specifically bound nucleic acid contaminants are an unwanted feature of recombinant RNA-binding proteins purified from Escherichia coli (E. coli). Removal of these contaminants represents an important step for the proteins' application in several biological assays and structural studies. The method described in this paper is a one-step protocol which is effective at removing tightly bound nucleic acids from overexpressed tagged HIV-1 Rev in E. coli. We combined affinity chromatography under denaturing conditions with subsequent on-column refolding, to prevent self-association of Rev while removing the nucleic acid contaminants from the end product. We compare this purification method with an established, multi-step protocol involving precipitation with polyethyleneimine (PEI). As our tailored protocol requires only one-step to simultaneously purify tagged proteins and eliminate bound cellular RNA and DNA, it represents a substantial advantage in time, effort, and expense.
Collapse
Affiliation(s)
- Marco Marenchino
- Medical University of South Carolina, Department of Biochemistry and Molecular Biology, 173 Ashley Avenue, BSB 535D, P.O. Box 250509, Charleston, SC 29425, USA
| | | | | |
Collapse
|
46
|
Non-coding RNA as a trigger of neuropathologic disorder phenotypes in transgenic Drosophila. J Neural Transm (Vienna) 2008; 115:1629-42. [PMID: 18779919 DOI: 10.1007/s00702-008-0078-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2008] [Accepted: 06/01/2008] [Indexed: 10/21/2022]
Abstract
At most, many protein-misfolding diseases develop as environmentally induced sporadic disorders. Recent studies indicate that the dynamic interplay between a wide repertoire of noncoding RNAs and the environment play an important role in brain development and pathogenesis of brain disorders. To elucidate this new issue, novel animal models which reproduce the most prominent disease manifestations are required. For this, transgenic Drosophila strains were constructed to express small highly structured, non-coding RNA under control of a heat shock promoter. Expression of the RNA induced formation of intracellular aggregates revealed by Thioflafin T in embryonic cell culture and Congo Red in the brain of transgenic flies. Also, this strongly perturbed the brain control of locomotion monitored by the parameters of sound production and memory retention of young 5-day-old males. This novel model demonstrates that expression of non-coding RNA alone is sufficient to trigger neuropathology.
Collapse
|
47
|
Affiliation(s)
- Jason R Thomas
- Department of Chemistry, Roger Adams Laboratory, University of Illinois, Urbana, Illinois 61822, USA
| | | |
Collapse
|
48
|
Prater CE, Saleh AD, Wear MP, Miller PS. Chimeric RNase H-competent oligonucleotides directed to the HIV-1 Rev response element. Bioorg Med Chem 2007; 15:5386-95. [PMID: 17566743 PMCID: PMC1987364 DOI: 10.1016/j.bmc.2007.05.066] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Revised: 05/23/2007] [Accepted: 05/29/2007] [Indexed: 11/26/2022]
Abstract
Chimeric oligo-2'-O-methylribonucleotides containing centrally located patches of contiguous 2'-deoxyribonucleotides and terminating in a nuclease resistant 3'-methylphosphonate internucleotide linkage were prepared. The oligonucleotides were targeted to the 3'-side of HIV Rev response element (RRE) stem-loop IIB RNA, which is adjacent to the high affinity Rev protein binding site and is critical to virus function. Thermal denaturation experiments showed that chimeric oligonucleotides form very stable duplexes with a complementary single-stranded RNA, and gel electrophoretic mobility shift assays (EMSA) showed that they bind with high affinity and specificity to RRE stem-loop II RNA (K(D) approximately 200 nM). The chimeric oligonucleotides promote RNase H-mediated hydrolysis of RRE stem-loop II RNA and have half-lives exceeding 24h when incubated in cell culture medium containing 10% fetal calf serum. One of the chimeric oligonucleotides inhibited RRE mediated expression of chloramphenicol acetyl transferase (CAT) approximately 60% at a concentration of 300 nM in HEK 293T cells co-transfected with p-RRE/CAT and p-Rev mammalian expression vectors.
Collapse
Affiliation(s)
| | | | | | - Paul S. Miller
- * Correspondence should be addressed to Paul S. Miller, . Phone: (410)-955-3489, Fax: (410)-955-2926
| |
Collapse
|
49
|
Kim H, Yin J. Effects of RNA splicing and post-transcriptional regulation on HIV-1 growth: a quantitative and integrated perspective. ACTA ACUST UNITED AC 2006; 152:138-52. [PMID: 16986277 DOI: 10.1049/ip-syb:20050004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Despite major advances over the last two decades in our understanding of RNA splicing and (post-) transcriptional regulation in human immunodeficiency virus type-1 (HIV-1), debate continues on the mechanisms and effects of Rev protein on HIV-1 growth. Moreover, arguments that HIV-1 has been optimised for growth have been largely based on speculation. Here, we begin systematically to address these issues by developing a detailed kinetic model for HIV-1 intracellular development. The model accounts for transcription, successive steps in RNA splicing, nuclear export of mRNAs, translation and shuttling of Rev and Tat, Tat-mediated transactivation of transcription, thresholds on Rev in its effects on nuclear export of mRNA, and inhibitory effects of Rev on splicing. Using the model, we found that inefficient splicing of HIV-1 mRNA was generally beneficial for HIV-1 growth, but that an excessive reduction in the splicing efficiency could be detrimental, suggesting that there exists a splicing efficiency that optimises HIV-1 growth. Further, we identified two key contributors to splicing efficiency, the intrinsic splicing rate and the extent of Rev-mediated splicing inhibition, and we showed how these should be balanced for HIV-1 to optimise its growth. Finally, we found that HIV-1 growth is relatively insensitive to different levels of the Rev export threshold, and we suggest that this mechanism evolved to delay viral growth, perhaps to enable evasion of host defensive responses. In summary, our model provides a quantitative and qualitative framework for probing how constituent mechanisms contribute to the complex, yet logical, process of HIV-1 growth.
Collapse
Affiliation(s)
- Hwijin Kim
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, NM 87545, USA
| | | |
Collapse
|
50
|
Michienzi A, De Angelis FG, Bozzoni I, Rossi JJ. A nucleolar localizing Rev binding element inhibits HIV replication. AIDS Res Ther 2006; 3:13. [PMID: 16712721 PMCID: PMC1513592 DOI: 10.1186/1742-6405-3-13] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2006] [Accepted: 05/19/2006] [Indexed: 11/25/2022] Open
Abstract
The Rev protein of the human immunodeficiency virus (HIV) facilitates the nuclear export of intron containing viral mRNAs allowing formation of infectious virions. Rev traffics through the nucleolus and shuttles between the nucleus and cytoplasm. Rev multimerization and interaction with the export protein CRM1 takes place in the nucleolus. To test the importance of Rev nucleolar trafficking in the HIV-1 replication cycle, we created a nucleolar localizing Rev Response Element (RRE) decoy and tested this for its anti-HIV activity. The RRE decoy provided marked inhibition of HIV-1 replication in both the CEM T-cell line and in primary CD34+ derived monocytes. These results demonstrate that titration of Rev in the nucleolus impairs HIV-1 replication and supports a functional role for Rev trafficking in this sub-cellular compartment.
Collapse
Affiliation(s)
- Alessandro Michienzi
- Division of Molecular Biology, Beckman Research Institute of the City of Hope, 1450 East Duarte Rd., Duarte, California 91010, USA
- Present address: Istituto Superiore di Sanita', Department of Cell Biology and Neuroscience, Viale Regina Elena 299, 00161, Rome, Italy
| | - Fernanda G De Angelis
- Istituto Pasteur, Fondazione Cenci-Bolognetti, Department of Genetics and Molecular Biology, University of Rome La Sapienza and IBPM of CNR, Rome, Italy
| | - Irene Bozzoni
- Istituto Pasteur, Fondazione Cenci-Bolognetti, Department of Genetics and Molecular Biology, University of Rome La Sapienza and IBPM of CNR, Rome, Italy
| | - John J Rossi
- Division of Molecular Biology, Beckman Research Institute of the City of Hope, 1450 East Duarte Rd., Duarte, California 91010, USA
- Division of Molecular Biology, Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, 1450 E. Duarte Rd., Duarte, CA 91010, USA
| |
Collapse
|