1
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Mackrill JJ. Non-inositol 1,4,5-trisphosphate (IP3) receptor IP3-binding proteins. BIOCHIMICA ET BIOPHYSICA ACTA (BBA) - MOLECULAR CELL RESEARCH 2023; 1870:119470. [PMID: 37011730 DOI: 10.1016/j.bbamcr.2023.119470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/23/2023] [Accepted: 03/23/2023] [Indexed: 04/03/2023]
Abstract
Conventionally, myo-D-inositol 1, 4,5-trisphosphate (IP3) is thought to exert its second messenger effects through the gating of IP3R Ca2+ release channels, located in Ca2+-storage organelles like the endoplasmic reticulum. However, there is considerable indirect evidence to support the concept that IP3 might interact with other, non-IP3R proteins within cells. To explore this possibility further, the Protein Data Bank was searched using the term "IP3". This resulted in the retrieval of 203 protein structures, the majority of which were members of the IP3R/ryanodine receptor superfamily of channels. Only 49 of these structures were complexed with IP3. These were inspected for their ability to interact with the carbon-1 phosphate of IP3, since this is the least accessible phosphate group of its precursor, phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2). This reduced the number of structures retrieved to 35, of which 9 were IP3Rs. The remaining 26 structures represent a diverse range of proteins, including inositol-lipid metabolizing enzymes, signal transducers, PH domain containing proteins, cytoskeletal anchor proteins, the TRPV4 ion channel, a retroviral Gag protein and fibroblast growth factor 2. Such proteins may impact on IP3 signalling and its effects on cell-biology. This represents an area open for exploration in the field of IP3 signalling.
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Affiliation(s)
- John James Mackrill
- Department of Physiology, University College Cork, Western Gateway Building, Western Road, Cork T12 XF62, Ireland.
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2
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Ghanam RH, Eastep GN, Saad JS. Structural Insights into the Mechanism of HIV-1 Tat Secretion from the Plasma Membrane. J Mol Biol 2023; 435:167880. [PMID: 36370804 PMCID: PMC9822876 DOI: 10.1016/j.jmb.2022.167880] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/27/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) trans-activator of transcription (Tat) is a small, intrinsically disordered basic protein that plays diverse roles in the HIV-1 replication cycle, including promotion of efficient viral RNA transcription. Tat is released by infected cells and subsequently absorbed by healthy cells, thereby contributing to HIV-1 pathogenesis including HIV-associated neurocognitive disorder. It has been shown that, in HIV-1-infected primary CD4 T-cells, Tat accumulates at the plasma membrane (PM) for secretion, a mechanism mediated by phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2). However, the structural basis for Tat interaction with the PM and thereby secretion is lacking. Herein, we employed NMR and biophysical methods to characterize Tat86 (86 amino acids) interactions with PI(4,5)P2 and lipid nanodiscs (NDs). Our data revealed that Arg49, Lys50 and Lys51 (RKK motif) constitute the PI(4,5)P2 binding site, that Tat86 interaction with lipid NDs is dependent on PI(4,5)P2 and phosphatidylserine (PS), and that the arginine-rich motif (RRQRRR) preferentially interacts with PS. Furthermore, we show that Trp11, previously implicated in Tat secretion, penetrates deeply in the membrane; substitution of Trp11 severely reduced Tat86 interaction with membranes. Deletion of the entire highly basic region and Trp11 completely abolished Tat86 binding to lipid NDs. Our data support a mechanism by which HIV-1 Tat secretion from the PM is mediated by a tripartite signal consisting of binding of the RKK motif to PI(4,5)P2, arginine-rich motif to PS, and penetration of Trp11 in the membrane. Altogether, these findings provide new insights into the molecular requirements for Tat binding to membranes during secretion.
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Affiliation(s)
- Ruba H Ghanam
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Gunnar N Eastep
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Jamil S Saad
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, United States.
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3
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Herrmann D, Hanson HM, Zhou LW, Addabbo R, Willkomm NA, Angert I, Mueller JD, Mansky LM, Saad JS. Molecular Determinants of Human T-cell Leukemia Virus Type 1 Gag Targeting to the Plasma Membrane for Assembly. J Mol Biol 2022; 434:167609. [PMID: 35490898 PMCID: PMC10557380 DOI: 10.1016/j.jmb.2022.167609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/20/2022] [Accepted: 04/23/2022] [Indexed: 01/10/2023]
Abstract
Assembly of human T-cell leukemia virus type 1 (HTLV-1) particles is initiated by the trafficking of virally encoded Gag polyproteins to the inner leaflet of the plasma membrane (PM). Gag-PM interactions are mediated by the matrix (MA) domain, which contains a myristoyl group (myr) and a basic patch formed by lysine and arginine residues. For many retroviruses, Gag-PM interactions are mediated by phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2]; however, previous studies suggested that HTLV-1 Gag-PM interactions and therefore virus assembly are less dependent on PI(4,5)P2. We have recently shown that PI(4,5)P2 binds directly to HTLV-1 unmyristoylated MA [myr(-)MA] and that myr(-)MA binding to membranes is significantly enhanced by inclusion of phosphatidylserine (PS) and PI(4,5)P2. Herein, we employed structural, biophysical, biochemical, mutagenesis, and cell-based assays to identify residues involved in MA-membrane interactions. Our data revealed that the lysine-rich motif (Lys47, Lys48, and Lys51) constitutes the primary PI(4,5)P2-binding site. Furthermore, we show that arginine residues 3, 7, 14 and 17 located in the unstructured N-terminus are essential for MA binding to membranes containing PS and/or PI(4,5)P2. Substitution of lysine and arginine residues severely attenuated virus-like particle production, but only the lysine residues could be clearly correlated with reduced PM binding. These results support a mechanism by which HTLV-1 Gag targeting to the PM is mediated by a trio engagement of the myr group, Arg-rich and Lys-rich motifs. These findings advance our understanding of a key step in retroviral particle assembly.
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Affiliation(s)
- Dominik Herrmann
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Heather M Hanson
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, United States
| | - Lynne W Zhou
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Rayna Addabbo
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, United States; School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, United States
| | - Nora A Willkomm
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, United States
| | - Isaac Angert
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, United States; School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, United States
| | - Joachim D Mueller
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, United States; School of Physics and Astronomy, University of Minnesota, Minneapolis, MN 55455, United States
| | - Louis M Mansky
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, United States.
| | - Jamil S Saad
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, United States.
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4
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Atomic view of the HIV-1 matrix lattice; implications on virus assembly and envelope incorporation. Proc Natl Acad Sci U S A 2022; 119:e2200794119. [PMID: 35658080 PMCID: PMC9191676 DOI: 10.1073/pnas.2200794119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
SignificanceThe assembly of immature HIV-1 particles is initiated by targeting of the Gag polyproteins to the plasma membrane (PM). Gag binding to the PM is mediated by the N-terminally myristoylated matrix (myrMA) domain. Formation of a Gag lattice on the PM is obligatory for the assembly of immature HIV-1 and envelope (Env) incorporation. The structure of the myrMA lattice presented here provided insights on the molecular factors that stabilize the lattice and hence favor Env incorporation. Our data support a mechanism for Gag binding to the PM during the assembly of immature particles and upon maturation. These findings advance our understanding of a critical step in HIV-1 assembly.
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5
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Herrmann D, Zhou LW, Hanson HM, Willkomm NA, Mansky LM, Saad JS. Structural Insights into the Mechanism of Human T-cell Leukemia Virus Type 1 Gag Targeting to the Plasma Membrane for Assembly. J Mol Biol 2021; 433:167161. [PMID: 34298060 PMCID: PMC8453114 DOI: 10.1016/j.jmb.2021.167161] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/10/2021] [Accepted: 07/12/2021] [Indexed: 01/10/2023]
Abstract
Retroviral Gag targeting to the plasma membrane (PM) for assembly is mediated by the N-terminal matrix (MA) domain. For many retroviruses, Gag-PM interaction is dependent on phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2). However, it has been shown that for human T-cell leukemia virus type 1 (HTLV-1), Gag binding to membranes is less dependent on PI(4,5)P2 than HIV-1, suggesting that other factors may modulate Gag assembly. To elucidate the mechanism by which HTLV-1 Gag binds to the PM, we employed NMR techniques to determine the structure of unmyristoylated MA (myr(-)MA) and to characterize its interactions with lipids and liposomes. The MA structure consists of four α-helices and unstructured N- and C-termini. We show that myr(-)MA binds to PI(4,5)P2 via the polar head and that binding to inositol phosphates (IPs) is significantly enhanced by increasing the number of phosphate groups on the inositol ring, indicating that the MA-IP binding is governed by charge-charge interactions. The IP binding site was mapped to a well-defined basic patch formed by lysine and arginine residues. Using an NMR-based liposome binding assay, we show that PI(4,5)P2and phosphatidylserine enhance myr(-)MA binding in a synergistic fashion. Confocal microscopy data revealed formation of puncta on the PM of Gag expressing cells. However, G2A-Gag mutant, lacking myristoylation, is diffuse and cytoplasmic. These results suggest that although myr(-)MA binds to membranes, myristoylation appears to be key for formation of HTLV-1 Gag puncta on the PM. Altogether, these findings advance our understanding of a key mechanism in retroviral assembly.
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Affiliation(s)
- Dominik Herrmann
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Lynne W Zhou
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Heather M Hanson
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA
| | - Nora A Willkomm
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA
| | - Louis M Mansky
- Institute for Molecular Virology, University of Minnesota - Twin Cities, Minneapolis, MN 55455, USA
| | - Jamil S Saad
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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6
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Lou F, Gao T, Han Z. Identification of putative key genes for thermal adaptation in the Japanese mantis shrimp (Oratosquilla oratoria) through population genomic analysis. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 39:100828. [PMID: 33838619 DOI: 10.1016/j.cbd.2021.100828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 03/19/2021] [Accepted: 03/21/2021] [Indexed: 10/21/2022]
Abstract
Little is known about the mechanisms underlying the relationship between genetic variation and the adaptation of Oratosquilla oratoria populations to different habitat temperature. Here, the genome-wide genetic information of three O. oratoria populations were obtained by IIB restriction site-associated DNA (2b-RAD) sequencing and 2403 single-nucleotide polymorphisms (SNPs) were identified. Based on the 2403 SNPs, we found a remarkable genetic differentiation between the Yellow Sea and the East China Sea groups of O. oratoria. Furthermore, 63 SNPs are thought to be associated with different sea temperatures. Based on the 63 SNPs, it is hypothesised that the long-term temperature differences may contribute to the variation of genes associated with multiple biological functions, such as material metabolism, cytoskeleton, cellular processes, inflammatory response and hormonal regulation. This study provides new information for elucidating the molecular mechanisms underlying the relationship between genetic variation and the adaptation of Oratosquilla oratoria populations to different temperature.
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Affiliation(s)
- Fangrui Lou
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China; School of Ocean, Yantai University, Yantai, Shandong 264005, China
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China
| | - Zhiqiang Han
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, China.
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7
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Eastep GN, Ghanam RH, Green TJ, Saad JS. Structural characterization of HIV-1 matrix mutants implicated in envelope incorporation. J Biol Chem 2021; 296:100321. [PMID: 33485964 PMCID: PMC7952133 DOI: 10.1016/j.jbc.2021.100321] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/05/2021] [Accepted: 01/20/2021] [Indexed: 11/28/2022] Open
Abstract
During the late phase of HIV-1 infection, viral Gag polyproteins are targeted to the plasma membrane (PM) for assembly. Gag localization at the PM is a prerequisite for the incorporation of the envelope protein (Env) into budding particles. Gag assembly and Env incorporation are mediated by the N-terminal myristoylated matrix (MA) domain of Gag. Nonconservative mutations in the trimer interface of MA (A45E, T70R, and L75G) were found to impair Env incorporation and infectivity, leading to the hypothesis that MA trimerization is an obligatory step for Env incorporation. Conversely, Env incorporation can be rescued by a compensatory mutation in the MA trimer interface (Q63R). The impact of these MA mutations on the structure and trimerization properties of MA is not known. In this study, we employed NMR spectroscopy, X-ray crystallography, and sedimentation techniques to characterize the structure and trimerization properties of HIV-1 MA A45E, Q63R, T70R, and L75G mutant proteins. NMR data revealed that these point mutations did not alter the overall structure and folding of MA but caused minor structural perturbations in the trimer interface. Analytical ultracentrifugation data indicated that mutations had a minimal effect on the MA monomer–trimer equilibrium. The high-resolution X-ray structure of the unmyristoylated MA Q63R protein revealed hydrogen bonding between the side chains of adjacent Arg-63 and Ser-67 on neighboring MA molecules, providing the first structural evidence for an additional intermolecular interaction in the trimer interface. These findings advance our knowledge of the interplay of MA trimerization and Env incorporation into HIV-1 particles.
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Affiliation(s)
- Gunnar N Eastep
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Ruba H Ghanam
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Todd J Green
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jamil S Saad
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA.
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8
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Wen Y, Feigenson GW, Vogt VM, Dick RA. Mechanisms of PI(4,5)P2 Enrichment in HIV-1 Viral Membranes. J Mol Biol 2020; 432:5343-5364. [PMID: 32739462 PMCID: PMC8262684 DOI: 10.1016/j.jmb.2020.07.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/12/2020] [Accepted: 07/26/2020] [Indexed: 01/10/2023]
Abstract
Phosphatidylinositol 4,5-bisphosphate (PIP2) is critical for HIV-1 virus assembly. The viral membrane is enriched in PIP2, suggesting that the virus assembles at PIP2-rich microdomains. We showed previously that in model membranes PIP2 can form nanoscopic clusters bridged by multivalent cations. Here, using purified proteins we quantitated the binding of HIV-1 Gag-related proteins to giant unilamellar vesicles containing either clustered or free PIP2. Myristoylated MA strongly preferred binding to clustered PIP2. By contrast, unmyristoylated HIV-1 MA, RSV MA, and a PH domain all preferred to interact with free PIP2. We also found that HIV-1 Gag multimerization promotes PIP2 clustering. Truncated Gag proteins comprising the MA, CA, and SP domains (MACASP) or the MA and CA domains (MACA) induced self-quenching of acyl chain-labeled fluorescent PIP2 in liposomes, implying clustering. However, HIV-1 MA itself did not induce PIP2 clustering. A CA inter-hexamer dimer interface mutation led to a loss of induced PIP2 clustering in MACA, indicating the importance of protein multimerization. Cryo-electron tomography of liposomes with bound MACA showed an amorphous protein layer on the membrane surface. Thus, it appears that while protein–protein interactions are required for PIP2 clustering, formation of a regular lattice is not. Protein-induced PIP2 clustering and multivalent cation-induced PIP2 clustering are additive. Taken together, these results provide the first evidence that HIV-1 Gag can selectively target pre-existing PIP2-enriched domains of the plasma membrane for viral assembly, and that Gag multimerization can further enrich PIP2 at assembly sites. These effects could explain the observed PIP2 enrichment in HIV-1.
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Affiliation(s)
- Yi Wen
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Gerald W Feigenson
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Volker M Vogt
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Robert A Dick
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY 14853, USA.
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9
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Li Q, Kang C. A Practical Perspective on the Roles of Solution NMR Spectroscopy in Drug Discovery. Molecules 2020; 25:molecules25132974. [PMID: 32605297 PMCID: PMC7411973 DOI: 10.3390/molecules25132974] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 06/21/2020] [Accepted: 06/26/2020] [Indexed: 11/26/2022] Open
Abstract
Solution nuclear magnetic resonance (NMR) spectroscopy is a powerful tool to study structures and dynamics of biomolecules under physiological conditions. As there are numerous NMR-derived methods applicable to probe protein–ligand interactions, NMR has been widely utilized in drug discovery, especially in such steps as hit identification and lead optimization. NMR is frequently used to locate ligand-binding sites on a target protein and to determine ligand binding modes. NMR spectroscopy is also a unique tool in fragment-based drug design (FBDD), as it is able to investigate target-ligand interactions with diverse binding affinities. NMR spectroscopy is able to identify fragments that bind weakly to a target, making it valuable for identifying hits targeting undruggable sites. In this review, we summarize the roles of solution NMR spectroscopy in drug discovery. We describe some methods that are used in identifying fragments, understanding the mechanism of action for a ligand, and monitoring the conformational changes of a target induced by ligand binding. A number of studies have proven that 19F-NMR is very powerful in screening fragments and detecting protein conformational changes. In-cell NMR will also play important roles in drug discovery by elucidating protein-ligand interactions in living cells.
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Affiliation(s)
- Qingxin Li
- Guangdong Provincial Engineering Laboratory of Biomass High Value Utilization, Guangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangzhou 510316, China
- Correspondence: (Q.L.); (C.K.); Tel.: +86-020-84168436 (Q.L.); +65-64070602 (C.K.)
| | - CongBao Kang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, Chromos, #05-01, Singapore 138670, Singapore
- Correspondence: (Q.L.); (C.K.); Tel.: +86-020-84168436 (Q.L.); +65-64070602 (C.K.)
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10
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Murphy RE, Saad JS. The Interplay between HIV-1 Gag Binding to the Plasma Membrane and Env Incorporation. Viruses 2020; 12:E548. [PMID: 32429351 PMCID: PMC7291237 DOI: 10.3390/v12050548] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/14/2020] [Accepted: 05/14/2020] [Indexed: 12/21/2022] Open
Abstract
Advancement in drug therapies and patient care have drastically improved the mortality rates of HIV-1 infected individuals. Many of these therapies were developed or improved upon by using structure-based techniques, which underscore the importance of understanding essential mechanisms in the replication cycle of HIV-1 at the structural level. One such process which remains poorly understood is the incorporation of the envelope glycoprotein (Env) into budding virus particles. Assembly of HIV particles is initiated by targeting of the Gag polyproteins to the inner leaflet of the plasma membrane (PM), a process mediated by the N-terminally myristoylated matrix (MA) domain and phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2). There is strong evidence that formation of the Gag lattice on the PM is a prerequisite for the incorporation of Env into budding particles. It is also suggested that Env incorporation is mediated by an interaction between its cytoplasmic tail (gp41CT) and the MA domain of Gag. In this review, we highlight the latest developments and current efforts to understand the interplay between gp41CT, MA, and the membrane during assembly. Elucidation of the molecular determinants of Gag-Env-membrane interactions may help in the development of new antiviral therapeutic agents that inhibit particle assembly, Env incorporation and ultimately virus production.
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Affiliation(s)
| | - Jamil S. Saad
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
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11
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Junková P, Pleskot R, Prchal J, Sýs J, Ruml T. Differences and commonalities in plasma membrane recruitment of the two morphogenetically distinct retroviruses HIV-1 and MMTV. J Biol Chem 2020; 295:8819-8833. [PMID: 32385109 DOI: 10.1074/jbc.ra119.011991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 05/05/2020] [Indexed: 11/06/2022] Open
Abstract
Retroviral Gag polyproteins are targeted to the inner leaflet of the plasma membrane through their N-terminal matrix (MA) domain. Because retroviruses of different morphogenetic types assemble their immature particles in distinct regions of the host cell, the mechanism of MA-mediated plasma membrane targeting differs among distinct retroviral morphogenetic types. Here, we focused on possible mechanistic differences of the MA-mediated plasma membrane targeting of the B-type mouse mammary tumor virus (MMTV) and C-type HIV-1, which assemble in the cytoplasm and at the plasma membrane, respectively. Molecular dynamics simulations, together with surface mapping, indicated that, similarly to HIV-1, MMTV uses a myristic switch to anchor the MA to the membrane and electrostatically interacts with phosphatidylinositol 4,5-bisphosphate to stabilize MA orientation. We observed that the affinity of MMTV MA to the membrane is lower than that of HIV-1 MA, possibly related to their different topologies and the number of basic residues in the highly basic MA region. The latter probably reflects the requirement of C-type retroviruses for tighter membrane binding, essential for assembly, unlike for D/B-type retroviruses, which assemble in the cytoplasm. A comparison of the membrane topology of the HIV-1 MA, using the surface-mapping method and molecular dynamics simulations, revealed that the residues at the HIV-1 MA C terminus help stabilize protein-protein interactions within the HIV-1 MA lattice at the plasma membrane. In summary, HIV-1 and MMTV share common features such as membrane binding of the MA via hydrophobic interactions and exhibit several differences, including lower membrane affinity of MMTV MA.
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Affiliation(s)
- Petra Junková
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic; Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Roman Pleskot
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Jan Prchal
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
| | - Jakub Sýs
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
| | - Tomáš Ruml
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic.
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12
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Watanabe SM, Strickland M, Tjandra N, Carter CA. RNA Binding Suppresses Tsg101 Recognition of Ub-Modified Gag and Facilitates Recruitment to the Plasma Membrane. Viruses 2020; 12:v12040447. [PMID: 32326417 PMCID: PMC7232412 DOI: 10.3390/v12040447] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/07/2020] [Accepted: 04/10/2020] [Indexed: 01/09/2023] Open
Abstract
The ESCRT-I factor Tsg101 is essential for sorting endocytic cargo and is exploited by viral pathogens to facilitate egress from cells. Both the nucleocapsid (NC) domain and p6 domain in HIV-1 Gag contribute to recruitment of the protein. However, the role of NC is unclear when the P(S/T)AP motif in p6 is intact, as the motif recruits Tsg101 directly. The zinc fingers in NC bind RNA and membrane and are critical for budding. Tsg101 can substitute for the distal ZnF (ZnF2) and rescue budding of a mutant made defective by deletion of this element. Here, we report that the ubiquitin (Ub) E2 variant (UEV) domain in Tsg101 binds tRNA in vitro. We confirmed that Tsg101 can substitute for ZnF2 when provided at the viral assembly site as a chimeric Gag-Tsg101 protein (Gag-ΔZnF2-Tsg101) and rescue budding. The UEV was not required in this context; however, mutation of the RNA binding determinants in UEV prevented Tsg101 recruitment from the cell interior when Gag and Tsg101 were co-expressed. The same Tsg101 mutations increased recognition of Gag-Ub, suggesting that tRNA and Ub compete for binding sites. This study identifies a novel Tsg101 binding partner that may contribute to its function in recognition of Ub-modified cargo.
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Affiliation(s)
- Susan M. Watanabe
- Department of Microbiology & Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794-5222, USA;
| | - Madeleine Strickland
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Nico Tjandra
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA;
- Correspondence: (N.T.); (C.A.C.); Tel.: +1-631-632-8801 (C.A.C.)
| | - Carol A. Carter
- Department of Microbiology & Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794-5222, USA;
- Correspondence: (N.T.); (C.A.C.); Tel.: +1-631-632-8801 (C.A.C.)
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13
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Fluorescent Protein Inserts in between NC and SP2 are Tolerated for Assembly, Release and Maturation of HIV with Limited Infectivity. Viruses 2019; 11:v11110973. [PMID: 31652757 PMCID: PMC6893430 DOI: 10.3390/v11110973] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/08/2019] [Accepted: 10/14/2019] [Indexed: 01/07/2023] Open
Abstract
We report the design of a fluorescent HIV construct that is labeled by insertion of fluorescent protein between the nucleocapsid (NC) and spacer peptide 2 (SP2) domains of Gag and further show that the fluorescent protein is released from its confines within Gag during maturation. This fluorescent HIV is capable of budding and maturation with similar efficiency to the parental virus. Virions generated using this design within the R8 HIV backbone pseudotyped with VSV-G were capable of delivering small RNA genomes encoding GFP to the target cells; however, the same design within the NL4-3 backbone has limited HIV infectivity. The virions generated by these constructs are approximately 165 ± 35 nm in size, which is significantly larger than wild type HIV. We suggest that this design has the potential to be a vehicle for protein and small guide RNA delivery.
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14
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Murphy RE, Samal AB, Vlach J, Mas V, Prevelige PE, Saad JS. Structural and biophysical characterizations of HIV-1 matrix trimer binding to lipid nanodiscs shed light on virus assembly. J Biol Chem 2019; 294:18600-18612. [PMID: 31640987 PMCID: PMC6901326 DOI: 10.1074/jbc.ra119.010997] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/16/2019] [Indexed: 12/17/2022] Open
Abstract
During the late phase of the HIV-1 replication cycle, the viral Gag polyproteins are targeted to the plasma membrane for assembly. The Gag-membrane interaction is mediated by binding of Gag's N-terminal myristoylated matrix (MA) domain to phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2). The viral envelope (Env) glycoprotein is then recruited to the assembly sites and incorporated into budding particles. Evidence suggests that Env incorporation is mediated by interactions between Gag's MA domain and the cytoplasmic tail of the gp41 subunit of Env (gp41CT). MA trimerization appears to be an obligatory step for this interaction. Insufficient production of a recombinant MA trimer and unavailability of a biologically relevant membrane system have been barriers to detailed structural and biophysical characterization of the putative MA-gp41CT-membrane interactions. Here, we engineered a stable recombinant HIV-1 MA trimer construct by fusing a foldon domain (FD) of phage T4 fibritin to the MA C terminus. Results from NMR experiments confirmed that the FD attachment does not adversely alter the MA structure. Employing hydrogen-deuterium exchange MS, we identified an MA-MA interface in the MA trimer that is implicated in Gag assembly and Env incorporation. Utilizing lipid nanodiscs as a membrane mimetic, we show that the MA trimer binds to membranes 30-fold tighter than does the MA monomer and that incorporation of PI(4,5)P2 and phosphatidylserine enhances the binding of MA to nanodiscs. These findings advance our understanding of a fundamental mechanism in HIV-1 assembly and provide a template for investigating the interaction of MA with gp41CT.
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Affiliation(s)
- R Elliot Murphy
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Alexandra B Samal
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Jiri Vlach
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Vicente Mas
- Centro Nacional de Microbiología and CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Peter E Prevelige
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Jamil S Saad
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294.
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15
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Watanabe SM, Medina GN, Eastep GN, Ghanam RH, Vlach J, Saad JS, Carter CA. The matrix domain of the Gag protein from avian sarcoma virus contains a PI(4,5)P 2-binding site that targets Gag to the cell periphery. J Biol Chem 2018; 293:18841-18853. [PMID: 30309982 DOI: 10.1074/jbc.ra118.003947] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 09/28/2018] [Indexed: 01/08/2023] Open
Abstract
The Gag protein of avian sarcoma virus (ASV) lacks an N-myristoyl (myr) group, but contains structural domains similar to those of HIV-1 Gag. Similarly to HIV-1, ASV Gag accumulates on the plasma membrane (PM) before egress; however, it is unclear whether the phospholipid PI(4,5)P2 binds directly to the matrix (MA) domain of ASV Gag, as is the case for HIV-1 Gag. Moreover, the role of PI(4,5)P2 in ASV Gag localization and budding has been controversial. Here, we report that substitution of residues that define the PI(4,5)P2-binding site in the ASV MA domain (reported in an accompanying paper) interfere with Gag localization to the cell periphery and inhibit the production of virus-like particles (VLPs). We show that co-expression of Sprouty2 (Spry2) or the pleckstrin homology domain of phospholipase Cδ (PH-PLC), two proteins that bind PI(4,5)P2, affects ASV Gag trafficking to the PM and budding. Replacement of the N-terminal 32 residues of HIV-1 MA, which encode its N-terminal myr signal and its PI(4,5)P2-binding site, with the structurally equivalent N-terminal 24 residues of ASV MA created a chimera that localized at the PM and produced VLPs. In contrast, the homologous PI(4,5)P2-binding signal in ASV MA could target HIV-1 Gag to the PM when substituted, but did not support budding. Collectively, these findings reveal a basic patch in both ASV and HIV-1 Gag capable of mediating PM binding and budding for ASV but not for HIV-1 Gag. We conclude that PI(4,5)P2 is a strong determinant of ASV Gag targeting to the PM and budding.
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Affiliation(s)
- Susan M Watanabe
- From the Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York 11794 and
| | - Gisselle N Medina
- From the Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York 11794 and
| | - Gunnar N Eastep
- the Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Ruba H Ghanam
- the Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Jiri Vlach
- the Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Jamil S Saad
- the Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Carol A Carter
- From the Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, New York 11794 and
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