1
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Aryal CM, Pan J. Probing the interactions of the HIV-1 matrix protein-derived polybasic region with lipid bilayers: insights from AFM imaging and force spectroscopy. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2024; 53:57-67. [PMID: 38172352 DOI: 10.1007/s00249-023-01697-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/18/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024]
Abstract
The human immunodeficiency virus type 1 (HIV-1) matrix protein contains a highly basic region, MA-HBR, crucial for various stages of viral replication. To elucidate the interactions between the polybasic peptide MA-HBR and lipid bilayers, we employed liquid-based atomic force microscopy (AFM) imaging and force spectroscopy on lipid bilayers of differing compositions. In 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayers, AFM imaging revealed the formation of annulus-shaped protrusions upon exposure to the polybasic peptide, accompanied by distinctive mechanical responses characterized by enhanced bilayer puncture forces. Importantly, our AFM-based force spectroscopy measurements unveiled that MA-HBR induces interleaflet decoupling within the cohesive bilayer organization. This is evidenced by a force discontinuity observed within the bilayer's elastic deformation regime. In POPC/cholesterol bilayers, MA-HBR caused similar yet smaller annular protrusions, demonstrating an intriguing interplay with cholesterol-rich membranes. In contrast, in bilayers containing anionic 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine (POPS) lipids, MA-HBR induced unique annular protrusions, granular nanoparticles, and nanotubules, showcasing its distinctive effects in anionic lipid-enriched environments. Notably, our force spectroscopy data revealed that anionic POPS lipids weakened interleaflet adhesion within the bilayer, resulting in interleaflet decoupling, which potentially contributes to the specific bilayer perturbations induced by MA-HBR. Collectively, our findings highlight the remarkable variations in how the polybasic peptide, MA-HBR, interacts with lipid bilayers of differing compositions, shedding light on its role in host membrane restructuring during HIV-1 infection.
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Affiliation(s)
- Chinta M Aryal
- Department of Physics, University of South Florida, Tampa, FL, 33620, USA
- , 2920 Burnet Ave Apt 3, Cincinnati, OH, 45219, USA
| | - Jianjun Pan
- Department of Physics, University of South Florida, Tampa, FL, 33620, USA.
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2
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Zhou AXZ, Hammond JA, Sheng K, Millar DP, Williamson JR. Early HIV-1 Gag Assembly on Lipid Membrane with vRNA. RESEARCH SQUARE 2023:rs.3.rs-3060076. [PMID: 37461524 PMCID: PMC10350206 DOI: 10.21203/rs.3.rs-3060076/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
HIV-1 capsid assembly is an essential process in the virus infection cycle. Initiation of capsid assembly involves viral proteins, genomic RNA, and the inner leaflet of the plasma membrane, facilitated by a number of cellular factors1. The viral structural protein Gag plays a number of central roles in this process, including association with the membrane, selective binding of genomic RNA, and oligomerization and packaging to ultimately produce an immature budded pro-viral particle2. While there have been intensive studies regarding the early stages of Gag assembly, there is a lack of consensus on the mechanism for nucleation and growth of Gag complexes3-7. Here we show that myristoylated Gag forms a trimer nucleus in a model membrane that can selectively bind a dimeric RNA containing the packaging signal. Subsequent growth of myristoyl-Gag oligomers requires vRNA, and occurs by addition of 1 or 2 Gag monomers at a time from solution. These data support a model where the immature capsid lattice formation occurs by a gradual lattice edge expansion, following a trimeric nucleation event. The dynamic single molecule data that support this model were recorded using mass photometry, involving full length myristoylated protein, RNA, and lipid together. These data are the first to support a lattice edge expansion model of Gag during early stages of assembly in a biological-relevant setting, providing insights to the fundamental models of virus structural protein assembly process.
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Affiliation(s)
- Anne X.-Z. Zhou
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - John A. Hammond
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - Kai Sheng
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - David P. Millar
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037, USA
| | - James R. Williamson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute; La Jolla, CA 92037, USA
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3
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Jin D, Zhu Y, Schubert HL, Goff SP, Musier-Forsyth K. HIV-1 Gag Binds the Multi-Aminoacyl-tRNA Synthetase Complex via the EPRS Subunit. Viruses 2023; 15:474. [PMID: 36851687 PMCID: PMC9967848 DOI: 10.3390/v15020474] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/31/2023] [Accepted: 01/31/2023] [Indexed: 02/11/2023] Open
Abstract
Host factor tRNAs facilitate the replication of retroviruses such as human immunodeficiency virus type 1 (HIV-1). HIV-1 uses human tRNALys3 as the primer for reverse transcription, and the assembly of HIV-1 structural protein Gag at the plasma membrane (PM) is regulated by matrix (MA) domain-tRNA interactions. A large, dynamic multi-aminoacyl-tRNA synthetase complex (MSC) exists in the cytosol and consists of eight aminoacyl-tRNA synthetases (ARSs) and three other cellular proteins. Proteomic studies to identify HIV-host interactions have identified the MSC as part of the HIV-1 Gag and MA interactomes. Here, we confirmed that the MA domain of HIV-1 Gag forms a stable complex with the MSC, mapped the primary interaction site to the linker domain of bi-functional human glutamyl-prolyl-tRNA synthetase (EPRS), and showed that the MA-EPRS interaction was RNA dependent. MA mutations that significantly reduced the EPRS interaction reduced viral infectivity and mapped to MA residues that also interact with phosphatidylinositol-(4,5)-bisphosphate. Overexpression of EPRS or EPRS fragments did not affect susceptibility to HIV-1 infection, and knockdown of EPRS reduced both a control reporter gene and HIV-1 protein translation. EPRS knockdown resulted in decreased progeny virion production, but the decrease could not be attributed to selective effects on virus gene expression, and the specific infectivity of the virions remained unchanged. While the precise function of the Gag-EPRS interaction remains uncertain, we discuss possible effects of the interaction on either virus or host activities.
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Affiliation(s)
- Danni Jin
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
| | - Yiping Zhu
- Departments of Biochemistry and Molecular Biophysics, and Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Heidi L. Schubert
- Department of Biochemistry, University of Utah, Salt Lake City, UT 841122, USA
| | - Stephen P. Goff
- Departments of Biochemistry and Molecular Biophysics, and Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
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4
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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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5
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Zhou AXZ, Hammond JA, Sheng K, Millar DP, Williamson JR. Early HIV-1 Gag Assembly on Lipid Membrane with vRNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.27.525415. [PMID: 36747785 PMCID: PMC9901173 DOI: 10.1101/2023.01.27.525415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Mass photometry (MP) was used to investigate the assembly of myristoylated full-length HIV-1 Gag (myr-Gag) and vRNA 5’ UTR fragment in a supported lipid bilayer (SLB) model system. The MP trajectories demonstrated that Gag trimerization on the membrane is a key step of early Gag assembly in the presence of vRNA. Growth of myr-Gag oligomers requires vRNA, occuring by addition of 1 or 2 monomers at a time from solution. These data support a model where formation of the Gag hexamers characteristic of the immature capsid lattice occurs by a gradual edge expansion, following a trimeric nucleation event. These dynamic single molecule data involving protein, RNA, and lipid components together, provide novel and fundamental insights into the initiation of virus capsid assembly.
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6
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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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7
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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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8
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Sumner C, Kotani O, Liu S, Musier-Forsyth K, Sato H, Ono A. Molecular Determinants in tRNA D-arm Required for Inhibition of HIV-1 Gag Membrane Binding. J Mol Biol 2022; 434:167390. [PMID: 34883117 PMCID: PMC8752508 DOI: 10.1016/j.jmb.2021.167390] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 11/23/2021] [Accepted: 11/30/2021] [Indexed: 02/01/2023]
Abstract
Plasma-membrane-specific localization of Gag, an essential step in HIV-1 particle assembly, is regulated by the interaction of the Gag MA domain with PI(4,5)P2 and tRNA-mediated inhibition of non-specific or premature membrane binding. Different tRNAs inhibit PI(4,5)P2-independent membrane binding to varying degrees in vitro; however, the structural determinants for this difference remain unknown. Here we demonstrate that membrane binding of full-length Gag synthesized in vitro using reticulocyte lysates is inhibited when RNAs that contain the anticodon arm of tRNAPro, but not that of tRNALys3, are added exogenously. In contrast, in the context of a liposome binding assay in which the effects of tRNAs on purified MA were tested, full-length tRNALys3 showed greater inhibition of MA membrane binding than full-length tRNAPro. While transplantation of the D loop sequence of tRNALys3 into tRNAPro resulted in a modest increase in the inhibitory effect relative to WT tRNAPro, replacing the entire D arm sequence with that of tRNALys3 was necessary to confer the full inhibitory effects upon tRNAPro. Together, these results demonstrate that the D arm of tRNALys3 is a major determinant of strong inhibition of MA membrane binding and that this inhibitory effect requires not only the D loop, which was recently reported to contact the MA highly basic region, but the loop sequence in the context of the D arm structure.
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Affiliation(s)
- Christopher Sumner
- Dept. of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, United States
| | - Osamu Kotani
- Center for Pathogen Genomics, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shuohui Liu
- Dept. of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, OH, United States
| | - Karin Musier-Forsyth
- Dept. of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, OH, United States
| | - Hironori Sato
- Center for Pathogen Genomics, National Institute of Infectious Diseases, Tokyo, Japan
| | - Akira Ono
- Dept. of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, United States
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9
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Abstract
Membrane proteins (MPs) play essential roles in numerous cellular processes. Because around 70% of the currently marketed drugs target MPs, a detailed understanding of their structure, binding properties, and functional dynamics in a physiologically relevant environment is crucial for a more detailed understanding of this important protein class. We here summarize the benefits of using lipid nanodiscs for NMR structural investigations and provide a detailed overview of the currently used lipid nanodisc systems as well as their applications in solution-state NMR. Despite the increasing use of other structural methods for the structure determination of MPs in lipid nanodiscs, solution NMR turns out to be a versatile tool to probe a wide range of MP features, ranging from the structure determination of small to medium-sized MPs to probing ligand and partner protein binding as well as functionally relevant dynamical signatures in a lipid nanodisc setting. We will expand on these topics by discussing recent NMR studies with lipid nanodiscs and work out a key workflow for optimizing the nanodisc incorporation of an MP for subsequent NMR investigations. With this, we hope to provide a comprehensive background to enable an informed assessment of the applicability of lipid nanodiscs for NMR studies of a particular MP of interest.
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Affiliation(s)
- Umut Günsel
- Bavarian NMR Center (BNMRZ) at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Strasse 2, 85748 Garching, Germany
| | - Franz Hagn
- Bavarian NMR Center (BNMRZ) at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Strasse 2, 85748 Garching, Germany.,Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
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10
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Bou-Nader C, Muecksch F, Brown JB, Gordon JM, York A, Peng C, Ghirlando R, Summers MF, Bieniasz PD, Zhang J. HIV-1 matrix-tRNA complex structure reveals basis for host control of Gag localization. Cell Host Microbe 2021; 29:1421-1436.e7. [PMID: 34384537 PMCID: PMC8650744 DOI: 10.1016/j.chom.2021.07.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/24/2021] [Accepted: 07/19/2021] [Indexed: 10/20/2022]
Abstract
The HIV-1 virion structural polyprotein, Gag, is directed to particle assembly sites at the plasma membrane by its N-terminal matrix (MA) domain. MA also binds to host tRNAs. To understand the molecular basis of MA-tRNA interaction and its potential function, we present a co-crystal structure of HIV-1 MA-tRNALys3 complex. The structure reveals a specialized group of MA basic and aromatic residues preconfigured to recognize the distinctive structure of the tRNA elbow. Mutational, cross-linking, fluorescence, and NMR analyses show that the crystallographically defined interface drives MA-tRNA binding in solution and living cells. The structure indicates that MA is unlikely to bind tRNA and membrane simultaneously. Accordingly, single-amino-acid substitutions that abolish MA-tRNA binding caused striking redistribution of Gag to the plasma membrane and reduced HIV-1 replication. Thus, HIV-1 exploits host tRNAs to occlude a membrane localization signal and control the subcellular distribution of its major structural protein.
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Affiliation(s)
- Charles Bou-Nader
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Janae B Brown
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Jackson M Gordon
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Ashley York
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Chen Peng
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Michael F Summers
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD 21250, USA; Howard Hughes Medical Institute, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA.
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA.
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11
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James EI, Murphree TA, Vorauer C, Engen JR, Guttman M. Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems. Chem Rev 2021; 122:7562-7623. [PMID: 34493042 PMCID: PMC9053315 DOI: 10.1021/acs.chemrev.1c00279] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Solution-phase hydrogen/deuterium
exchange (HDX) coupled to mass
spectrometry (MS) is a widespread tool for structural analysis across
academia and the biopharmaceutical industry. By monitoring the exchangeability
of backbone amide protons, HDX-MS can reveal information about higher-order
structure and dynamics throughout a protein, can track protein folding
pathways, map interaction sites, and assess conformational states
of protein samples. The combination of the versatility of the hydrogen/deuterium
exchange reaction with the sensitivity of mass spectrometry has enabled
the study of extremely challenging protein systems, some of which
cannot be suitably studied using other techniques. Improvements over
the past three decades have continually increased throughput, robustness,
and expanded the limits of what is feasible for HDX-MS investigations.
To provide an overview for researchers seeking to utilize and derive
the most from HDX-MS for protein structural analysis, we summarize
the fundamental principles, basic methodology, strengths and weaknesses,
and the established applications of HDX-MS while highlighting new
developments and applications.
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Affiliation(s)
- Ellie I James
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Taylor A Murphree
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Clint Vorauer
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - John R Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
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12
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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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13
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Schmidpeter PAM, Nimigean CM. Correlating ion channel structure and function. Methods Enzymol 2021; 652:3-30. [PMID: 34059287 DOI: 10.1016/bs.mie.2021.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Recent developments in cryogenic electron microscopy (cryo-EM) led to an exponential increase in high-resolution structures of membrane proteins, and in particular ion channels. However, structures alone can only provide limited information about the workings of these proteins. In order to understand ion channel function and regulation in molecular detail, the obtained structural data need to be correlated to functional states of the same protein. Here, we describe several techniques that can be employed to study ion channel structure and function in vitro and under defined, similar conditions. Lipid nanodiscs provide a native-like environment for membrane proteins and have become a valuable tool in membrane protein structural biology and biophysics. Combined with liposome-based flux assays for the kinetic analysis of ion channel activity as well as electrophysiological recordings, researchers now have access to an array of experimental techniques allowing for detailed structure-function correlations using purified components. Two examples are presented where we put emphasis on the lipid environment and time-resolved techniques together with mutations and protein engineering to interpret structural data obtained from single particle cryo-EM on cyclic nucleotide-gated or Ca2+-gated K+ channels. Furthermore, we provide short protocols for all the assays used in our work so that others can adapt these techniques to their experimental needs. Comprehensive structure-function correlations are essential in order to pharmacologically target channelopathies.
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Affiliation(s)
| | - Crina M Nimigean
- Department of Anesthesiology, Weill Cornell Medicine, New York, NY, United States.
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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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15
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Meusser B, Purfuerst B, Luft FC. HIV-1 Gag release from yeast reveals ESCRT interaction with the Gag N-terminal protein region. J Biol Chem 2020; 295:17950-17972. [PMID: 32994219 PMCID: PMC7939435 DOI: 10.1074/jbc.ra120.014710] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 09/25/2020] [Indexed: 11/30/2022] Open
Abstract
The HIV-1 protein Gag assembles at the plasma membrane and drives virion budding, assisted by the cellular endosomal complex required for transport (ESCRT) proteins. Two ESCRT proteins, TSG101 and ALIX, bind to the Gag C-terminal p6 peptide. TSG101 binding is important for efficient HIV-1 release, but how ESCRTs contribute to the budding process and how their activity is coordinated with Gag assembly is poorly understood. Yeast, allowing genetic manipulation that is not easily available in human cells, has been used to characterize the cellular ESCRT function. Previous work reported Gag budding from yeast spheroplasts, but Gag release was ESCRT-independent. We developed a yeast model for ESCRT-dependent Gag release. We combined yeast genetics and Gag mutational analysis with Gag-ESCRT binding studies and the characterization of Gag-plasma membrane binding and Gag release. With our system, we identified a previously unknown interaction between ESCRT proteins and the Gag N-terminal protein region. Mutations in the Gag-plasma membrane-binding matrix domain that reduced Gag-ESCRT binding increased Gag-plasma membrane binding and Gag release. ESCRT knockout mutants showed that the release enhancement was an ESCRT-dependent effect. Similarly, matrix mutation enhanced Gag release from human HEK293 cells. Release enhancement partly depended on ALIX binding to p6, although binding site mutation did not impair WT Gag release. Accordingly, the relative affinity for matrix compared with p6 in GST-pulldown experiments was higher for ALIX than for TSG101. We suggest that a transient matrix-ESCRT interaction is replaced when Gag binds to the plasma membrane. This step may activate ESCRT proteins and thereby coordinate ESCRT function with virion assembly.
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Affiliation(s)
- Birgit Meusser
- Charité Medical Faculty, Berlin, Germany; Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | | | - Friedrich C Luft
- Charité Medical Faculty, Berlin, Germany; Max-Delbrück-Center for Molecular Medicine, Berlin, Germany; Experimental and Clinical Research Center, Berlin, Germany.
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16
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Boyd PS, Brown JB, Brown JD, Catazaro J, Chaudry I, Ding P, Dong X, Marchant J, O’Hern CT, Singh K, Swanson C, Summers MF, Yasin S. NMR Studies of Retroviral Genome Packaging. Viruses 2020; 12:v12101115. [PMID: 33008123 PMCID: PMC7599994 DOI: 10.3390/v12101115] [Citation(s) in RCA: 4] [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: 08/04/2020] [Revised: 09/18/2020] [Accepted: 09/26/2020] [Indexed: 12/03/2022] Open
Abstract
Nearly all retroviruses selectively package two copies of their unspliced RNA genomes from a cellular milieu that contains a substantial excess of non-viral and spliced viral RNAs. Over the past four decades, combinations of genetic experiments, phylogenetic analyses, nucleotide accessibility mapping, in silico RNA structure predictions, and biophysical experiments were employed to understand how retroviral genomes are selected for packaging. Genetic studies provided early clues regarding the protein and RNA elements required for packaging, and nucleotide accessibility mapping experiments provided insights into the secondary structures of functionally important elements in the genome. Three-dimensional structural determinants of packaging were primarily derived by nuclear magnetic resonance (NMR) spectroscopy. A key advantage of NMR, relative to other methods for determining biomolecular structure (such as X-ray crystallography), is that it is well suited for studies of conformationally dynamic and heterogeneous systems—a hallmark of the retrovirus packaging machinery. Here, we review advances in understanding of the structures, dynamics, and interactions of the proteins and RNA elements involved in retroviral genome selection and packaging that are facilitated by NMR.
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Rendezvous at Plasma Membrane: Cellular Lipids and tRNA Set up Sites of HIV-1 Particle Assembly and Incorporation of Host Transmembrane Proteins. Viruses 2020; 12:v12080842. [PMID: 32752131 PMCID: PMC7472227 DOI: 10.3390/v12080842] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 07/20/2020] [Accepted: 07/24/2020] [Indexed: 12/28/2022] Open
Abstract
The HIV-1 structural polyprotein Gag drives the virus particle assembly specifically at the plasma membrane (PM). During this process, the nascent virion incorporates specific subsets of cellular lipids and host membrane proteins, in addition to viral glycoproteins and viral genomic RNA. Gag binding to the PM is regulated by cellular factors, including PM-specific phospholipid PI(4,5)P2 and tRNAs, both of which bind the highly basic region in the matrix domain of Gag. In this article, we review our current understanding of the roles played by cellular lipids and tRNAs in specific localization of HIV-1 Gag to the PM. Furthermore, we examine the effects of PM-bound Gag on the organization of the PM bilayer and discuss how the reorganization of the PM at the virus assembly site potentially contributes to the enrichment of host transmembrane proteins in the HIV-1 particle. Since some of these host transmembrane proteins alter release, attachment, or infectivity of the nascent virions, the mechanism of Gag targeting to the PM and the nature of virus assembly sites have major implications in virus spread.
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18
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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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19
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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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