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Interplay between Host tRNAs and HIV-1: A Structural Perspective. Viruses 2021; 13:v13091819. [PMID: 34578400 PMCID: PMC8473020 DOI: 10.3390/v13091819] [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: 08/12/2021] [Revised: 09/06/2021] [Accepted: 09/09/2021] [Indexed: 12/23/2022] Open
Abstract
The cellular metabolism of host tRNAs and life cycle of HIV-1 cross paths at several key virus-host interfaces. Emerging data suggest a multi-faceted interplay between host tRNAs and HIV-1 that plays essential roles, both structural and regulatory, in viral genome replication, genome packaging, and virion biogenesis. HIV-1 not only hijacks host tRNAs and transforms them into obligatory reverse transcription primers but further commandeers tRNAs to regulate the localization of its major structural protein, Gag, via a specific interface. This review highlights recent advances in understanding tRNA-HIV-1 interactions, primarily from a structural perspective, which start to elucidate their underlying molecular mechanisms, intrinsic specificities, and biological significances. Such understanding may provide new avenues toward developing HIV/AIDS treatments and therapeutics including small molecules and RNA biologics that target these host-virus interfaces.
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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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3
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Li CW, Chen BS. Investigating HIV-Human Interaction Networks to Unravel Pathogenic Mechanism for Drug Discovery: A Systems Biology Approach. Curr HIV Res 2019; 16:77-95. [PMID: 29468972 DOI: 10.2174/1570162x16666180219155324] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 01/18/2018] [Accepted: 02/14/2018] [Indexed: 02/08/2023]
Abstract
BACKGROUND Two big issues in the study of pathogens are determining how pathogens infect hosts and how the host defends itself against infection. Therefore, investigating host-pathogen interactions is important for understanding pathogenicity and host defensive mechanisms and treating infections. METHODS In this study, we used omics data, including time-course data from high-throughput sequencing, real-time polymerase chain reaction, and human microRNA (miRNA) and protein-protein interaction to construct an interspecies protein-protein and miRNA interaction (PPMI) network of human CD4+ T cells during HIV-1 infection through system modeling and identification. RESULTS By applying a functional annotation tool to the identified PPMI network at each stage of HIV infection, we found that repressions of three miRNAs, miR-140-5p, miR-320a, and miR-941, are involved in the development of autoimmune disorders, tumor proliferation, and the pathogenesis of T cells at the reverse transcription stage. Repressions of miR-331-3p and miR-320a are involved in HIV-1 replication, replicative spread, anti-apoptosis, cell proliferation, and dysregulation of cell cycle control at the integration/replication stage. Repression of miR-341-5p is involved in carcinogenesis at the late stage of HIV-1 infection. CONCLUSION By investigating the common core proteins and changes in specific proteins in the PPMI network between the stages of HIV-1 infection, we obtained pathogenic insights into the functional core modules and identified potential drug combinations for treating patients with HIV-1 infection, including thalidomide, oxaprozin, and metformin, at the reverse transcription stage; quercetin, nifedipine, and fenbendazole, at the integration/replication stage; and staurosporine, quercetin, prednisolone, and flufenamic acid, at the late stage.
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Affiliation(s)
- Cheng-Wei Li
- Laboratory of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Bor-Sen Chen
- Laboratory of Control and Systems Biology, Department of Electrical Engineering, National Tsing Hua University, Hsinchu, Taiwan
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4
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Structural characterization of human aminoacyl-tRNA synthetases for translational and nontranslational functions. Methods 2017; 113:83-90. [DOI: 10.1016/j.ymeth.2016.11.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 11/14/2016] [Accepted: 11/21/2016] [Indexed: 11/18/2022] Open
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5
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Xiao X, Agris PF, Hall CK. Designing peptide sequences in flexible chain conformations to bind RNA: a search algorithm combining Monte Carlo, self-consistent mean field and concerted rotation techniques. J Chem Theory Comput 2016; 11:740-52. [PMID: 26579605 DOI: 10.1021/ct5008247] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A search algorithm combining Monte Carlo, self-consistent mean field, and concerted rotation techniques was developed to discover peptide sequences that are reasonable HIV drug candidates due to their exceptional binding to human tRNAUUU(Lys3), the primer of HIV replication. The search algorithm allows for iteration between sequence mutations and conformation changes during sequence evolution. Searches conducted for different classes of peptides identified several potential peptide candidates. Analysis of the energy revealed that the asparagine and cysteine at residues 11 and 12 play important roles in "recognizing" tRNA(Lys3) via van der Waals interactions, contributing to binding specificity. Arginines preferentially attract the phosphate linkage via charge-charge interaction, contributing to binding affinity. Evaluation of the RNA/peptide complex's structure revealed that adding conformation changes to the search algorithm yields peptides with better binding affinity and specificity to tRNA(Lys3) than a previous mutation-only algorithm.
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Affiliation(s)
- Xingqing Xiao
- Chemical and Biomolecular Engineering Department, North Carolina State University , Raleigh, North Carolina 27695-7905, United States
| | - Paul F Agris
- The RNA Institute, University at Albany, State University of New York , Albany, New York 12222, United States
| | - Carol K Hall
- Chemical and Biomolecular Engineering Department, North Carolina State University , Raleigh, North Carolina 27695-7905, United States
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Xiao X, Agris PF, Hall CK. Introducing folding stability into the score function for computational design of RNA-binding peptides boosts the probability of success. Proteins 2016; 84:700-11. [PMID: 26914059 DOI: 10.1002/prot.25021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 01/26/2016] [Accepted: 02/10/2016] [Indexed: 12/30/2022]
Abstract
A computational strategy that integrates our peptide search algorithm with atomistic molecular dynamics simulation was used to design rational peptide drugs that recognize and bind to the anticodon stem and loop domain (ASL(Lys3)) of human tRNAUUULys3 for the purpose of interrupting HIV replication. The score function of the search algorithm was improved by adding a peptide stability term weighted by an adjustable factor λ to the peptide binding free energy. The five best peptide sequences associated with five different values of λ were determined using the search algorithm and then input in atomistic simulations to examine the stability of the peptides' folded conformations and their ability to bind to ASL(Lys3). Simulation results demonstrated that setting an intermediate value of λ achieves a good balance between optimizing the peptide's binding ability and stabilizing its folded conformation during the sequence evolution process, and hence leads to optimal binding to the target ASL(Lys3). Thus, addition of a peptide stability term significantly improves the success rate for our peptide design search.
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Affiliation(s)
- Xingqing Xiao
- Chemical and Biomolecular Engineering Department, North Carolina State University, Raleigh, North Carolina, 27695-7905
| | - Paul F Agris
- The RNA Institute, University at Albany, State University of New York, Albany, New York, 12222
| | - Carol K Hall
- Chemical and Biomolecular Engineering Department, North Carolina State University, Raleigh, North Carolina, 27695-7905
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Abstract
When compared to other conserved housekeeping protein families, such as ribosomal proteins, during the evolution of higher eukaryotes, aminoacyl-tRNA synthetases (aaRSs) show an apparent high propensity to add new sequences, and especially new domains. The stepwise emergence of those new domains is consistent with their involvement in a broad range of biological functions beyond protein synthesis, and correlates with the increasing biological complexity of higher organisms. These new domains have been extensively characterized based on their evolutionary origins and their sequence, structural, and functional features. While some of the domains are uniquely found in aaRSs and may have originated from nucleic acid binding motifs, others are common domain modules mediating protein-protein interactions that play a critical role in the assembly of the multi-synthetase complex (MSC). Interestingly, the MSC has emerged from a miniature complex in yeast to a large stable complex in humans. The human MSC consists of nine aaRSs (LysRS, ArgRS, GlnRS, AspRS, MetRS, IleRS, LeuRS, GluProRS, and bifunctional aaRs) and three scaffold proteins (AIMP1/p43, AIMP2/p38, and AIMP3/p18), and has a molecular weight of 1.5 million Dalton. The MSC has been proposed to have a functional dualism: facilitating protein synthesis and serving as a reservoir of non-canonical functions associated with its synthetase and non-synthetase components. Importantly, domain additions and functional expansions are not limited to the components of the MSC and are found in almost all aaRS proteins. From a structural perspective, multi-functionalities are represented by multiple conformational states. In fact, alternative conformations of aaRSs have been generated by various mechanisms from proteolysis to alternative splicing and posttranslational modifications, as well as by disease-causing mutations. Therefore, the metamorphosis between different conformational states is connected to the activation and regulation of the novel functions of aaRSs in higher eukaryotes.
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Affiliation(s)
- Min Guo
- Department of Cancer Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33410, USA,
| | - Xiang-Lei Yang
- Department of Cancer Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA,
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Roberts VA, Thompson EE, Pique ME, Perez MS, Ten Eyck LF. DOT2: Macromolecular docking with improved biophysical models. J Comput Chem 2013; 34:1743-58. [PMID: 23695987 PMCID: PMC4370774 DOI: 10.1002/jcc.23304] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 02/20/2013] [Accepted: 04/07/2013] [Indexed: 12/11/2022]
Abstract
Computational docking is a useful tool for predicting macromolecular complexes, which are often difficult to determine experimentally. Here, we present the DOT2 software suite, an updated version of the DOT intermolecular docking program. DOT2 provides straightforward, automated construction of improved biophysical models based on molecular coordinates, offering checkpoints that guide the user to include critical features. DOT has been updated to run more quickly, allow flexibility in grid size and spacing, and generate an infinitive complete list of favorable candidate configurations. Output can be filtered by experimental data and rescored by the sum of electrostatic and atomic desolvation energies. We show that this rescoring method improves the ranking of correct complexes for a wide range of macromolecular interactions and demonstrate that biologically relevant models are essential for biologically relevant results. The flexibility and versatility of DOT2 accommodate realistic models of complex biological systems, improving the likelihood of a successful docking outcome.
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Affiliation(s)
- Victoria A Roberts
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, California 92093, USA.
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Dewan V, Reader J, Forsyth KM. Role of aminoacyl-tRNA synthetases in infectious diseases and targets for therapeutic development. Top Curr Chem (Cham) 2013; 344:293-329. [PMID: 23666077 DOI: 10.1007/128_2013_425] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Aminoacyl-tRNA synthetases (AARSs) play a pivotal role in protein synthesis and cell viability. These 22 "housekeeping" enzymes (1 for each standard amino acid plus pyrrolysine and o-phosphoserine) are specifically involved in recognizing and aminoacylating their cognate tRNAs in the cellular pool with the correct amino acid prior to delivery of the charged tRNA to the protein synthesis machinery. Besides serving this canonical function, higher eukaryotic AARSs, some of which are organized in the cytoplasm as a multisynthetase complex of nine enzymes plus additional cellular factors, have also been implicated in a variety of non-canonical roles. AARSs are involved in the regulation of transcription, translation, and various signaling pathways, thereby ensuring cell survival. Based in part on their versatility, AARSs have been recruited by viruses to perform essential functions. For example, host synthetases are packaged into some retroviruses and are required for their replication. Other viruses mimic tRNA-like structures in their genomes, and these motifs are aminoacylated by the host synthetase as part of the viral replication cycle. More recently, it has been shown that certain large DNA viruses infecting animals and other diverse unicellular eukaryotes encode tRNAs, AARSs, and additional components of the protein-synthesis machinery. This chapter will review our current understanding of the role of host AARSs and tRNA-like structures in viruses and discuss their potential as anti-viral drug targets. The identification and development of compounds that target bacterial AARSs, thereby serving as novel antibiotics, will also be discussed. Particular attention will be given to recent work on a number of tRNA-dependent AARS inhibitors and to advances in a new class of natural "pro-drug" antibiotics called Trojan Horse inhibitors. Finally, we will explore how bacteria that naturally produce AARS-targeting antibiotics must protect themselves against cell suicide using naturally antibiotic resistant AARSs, and how horizontal gene transfer of these AARS genes to pathogens may threaten the future use of this class of antibiotics.
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Affiliation(s)
- Varun Dewan
- Department of Chemistry and Biochemistry, Ohio State Biochemistry Program, Center for RNA Biology, and Center for Retroviral Research, The Ohio State University, Columbus, OH, 43210, USA
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Dewan V, Wei M, Kleiman L, Musier-Forsyth K. Dual role for motif 1 residues of human lysyl-tRNA synthetase in dimerization and packaging into HIV-1. J Biol Chem 2012; 287:41955-62. [PMID: 23095741 DOI: 10.1074/jbc.m112.421842] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The primer for reverse transcription in human immunodeficiency virus type 1, human tRNA(Lys,3), is selectively packaged into the virion along with tRNA(Lys1,2). Human lysyl-tRNA synthetase (hLysRS), the only cellular factor known to interact specifically with all three tRNA(Lys) isoacceptors, is also selectively packaged into HIV-1. We have previously defined a tRNA(Lys) packaging complex that includes the tRNA(Lys) isoacceptors, LysRS, HIV-1 Gag, GagPol, and viral RNA. Numerous studies support the hypothesis that during tRNA(Lys) packaging, a Gag·GagPol complex interacts with a tRNA(Lys)·LysRS complex, with Gag interacting specifically with the catalytic domain of LysRS, and GagPol interacting with both Gag and tRNA(Lys). In this work, we have identified residues along one face of the motif 1 dimerization helix (H7) of hLysRS that are critical for packaging of the synthetase into virions. Mutation of these residues affects binding to Gag in vitro, as well as the oligomerization state and aminoacylation activity of the synthetase. Taken together, these data suggest that H7 of LysRS has a dual function. In its canonical role it maintains the synthetase dimer interface, whereas in its function in tRNA primer recruitment, it bridges interactions with HIV-1 Gag.
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Affiliation(s)
- Varun Dewan
- Department of Chemistry and Biochemistry, Ohio State Biochemistry Program, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
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11
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Dewan V, Liu T, Chen KM, Qian Z, Xiao Y, Kleiman L, Mahasenan KV, Li C, Matsuo H, Pei D, Musier-Forsyth K. Cyclic peptide inhibitors of HIV-1 capsid-human lysyl-tRNA synthetase interaction. ACS Chem Biol 2012; 7:761-9. [PMID: 22276994 PMCID: PMC3330833 DOI: 10.1021/cb200450w] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
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The human immunodeficiency virus type 1 (HIV-1) capsid
protein
(CA) plays a critical role in the viral life cycle. The C-terminal
domain (CTD) of CA binds to human lysyl-tRNA synthetase (hLysRS),
and this interaction facilitates packaging of host cell tRNALys,3, which serves as the primer for reverse transcription. Here, we
report the library synthesis, high-throughput screening, and identification
of cyclic peptides (CPs) that bind HIV-1 CA. Scrambling or single-residue
changes of the selected peptide sequences eliminated binding, suggesting
a sequence-specific mode of interaction. Two peptides (CP2 and CP4)
subjected to detailed analysis also inhibited hLysRS/CA interaction in vitro. Nuclear magnetic resonance spectroscopy and mutagenesis
studies revealed that both CPs bind to a site proximal to helix 4
of the CA-CTD, which is the known site of hLysRS interaction. These
results extend the current repertoire of CA-binding molecules to a
new class of peptides targeting a novel site with potential for development
into novel antiviral agents.
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Affiliation(s)
| | | | - Kuan-Ming Chen
- Biochemistry, Molecular
Biology
and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | | | - Yong Xiao
- Lady Davis Institute for Medical
Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec, Canada H3T 1E2
| | - Lawrence Kleiman
- Lady Davis Institute for Medical
Research and McGill AIDS Centre, Jewish General Hospital, Montreal, Quebec, Canada H3T 1E2
| | | | | | - Hiroshi Matsuo
- Biochemistry, Molecular
Biology
and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
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Vo MN, Yang XL, Schimmel P. Dissociating quaternary structure regulates cell-signaling functions of a secreted human tRNA synthetase. J Biol Chem 2011; 286:11563-8. [PMID: 21310955 DOI: 10.1074/jbc.c110.213876] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Many tRNA synthetases are homodimers that are catalytically inactive as monomers. An example is the 528-amino acid human tyrosyl-tRNA synthetase, which is made up of an N-terminal catalytic unit (TyrRS(Mini)) and a 164-amino acid C-domain. Although native TyrRS has no known cytokine functions, natural proteolysis of secreted TyrRS releases TyrRS(Mini), which not only has the same aminoacylation activity as native TyrRS but also has strong activity for stimulating migration of polymorphonuclear leukocytes. The migration-stimulating activity is dependent on an ELR tripeptide motif, similar to that in CXC cytokines like IL-8, and also has the familiar bell-shaped concentration dependence seen for CXC cytokines. Here we show that in contrast to IL-8, where the bell-shaped dependence arises from the effects of CXCR1/2 receptor internalization, TyrRS(Mini) does not induce internalization of CXCR1/2. A rationally designed non-associating monomer and a non-dissociating dimer were constructed. With these constructs, the bell-shaped concentration dependence of leukocyte migration was shown to arise from the agonist (for migration) activity of the catalytically inactive monomer and the antagonist activity of the catalytically active dimer. Thus, the dissociating quaternary structure of TyrRS(Mini) regulates two opposing cytokine activities and suggests the possibility of dissociating quaternary structures regulating novel functions of other tRNA synthetases.
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Affiliation(s)
- My-Nuong Vo
- Skaggs Institute for Chemical Biology and Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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