1
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Khatkar P, Mensah G, Ning S, Cowen M, Kim Y, Williams A, Abulwerdi FA, Zhao Y, Zeng C, Le Grice SFJ, Kashanchi F. HIV-1 Transcription Inhibition Using Small RNA-Binding Molecules. Pharmaceuticals (Basel) 2023; 17:33. [PMID: 38256867 PMCID: PMC10819208 DOI: 10.3390/ph17010033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 12/11/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
The HIV-1 transactivator protein Tat interacts with the transactivation response element (TAR) at the three-nucleotide UCU bulge to facilitate the recruitment of transcription elongation factor-b (P-TEFb) and induce the transcription of the integrated proviral genome. Therefore, the Tat-TAR interaction, unique to the virus, is a promising target for developing antiviral therapeutics. Currently, there are no FDA-approved drugs against HIV-1 transcription, suggesting the need to develop novel inhibitors that specifically target HIV-1 transcription. We have identified potential candidates that effectively inhibit viral transcription in myeloid and T cells without apparent toxicity. Among these candidates, two molecules showed inhibition of viral protein expression. A molecular docking and simulation approach was used to determine the binding dynamics of these small molecules on TAR RNA in the presence of the P-TEFb complex, which was further validated by a biotinylated RNA pulldown assay. Furthermore, we examined the effect of these molecules on transcription factors, including the SWI/SNF complex (BAF or PBAF), which plays an important role in chromatin remodeling near the transcription start site and hence regulates virus transcription. The top candidates showed significant viral transcription inhibition in primary cells infected with HIV-1 (98.6). Collectively, our study identified potential transcription inhibitors that can potentially complement existing cART drugs to address the current therapeutic gap in current regimens. Additionally, shifting of the TAR RNA loop towards Cyclin T1 upon molecule binding during molecular simulation studies suggested that targeting the TAR loop and Tat-binding UCU bulge together should be an essential feature of TAR-binding molecules/inhibitors to achieve complete viral transcription inhibition.
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Affiliation(s)
- Pooja Khatkar
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA; (P.K.)
| | - Gifty Mensah
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA; (P.K.)
| | - Shangbo Ning
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan 430079, China
| | - Maria Cowen
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA; (P.K.)
| | - Yuriy Kim
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA; (P.K.)
| | - Anastasia Williams
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA; (P.K.)
| | | | - Yunjie Zhao
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan 430079, China
| | - Chen Zeng
- Physics Department, The George Washington University, Washington, DC 20052, USA
| | | | - Fatah Kashanchi
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA 20110, USA; (P.K.)
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2
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Camara MB, Sobeh AM, Eichhorn CD. Progress in 7SK ribonucleoprotein structural biology. Front Mol Biosci 2023; 10:1154622. [PMID: 37051324 PMCID: PMC10083321 DOI: 10.3389/fmolb.2023.1154622] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/16/2023] [Indexed: 03/29/2023] Open
Abstract
The 7SK ribonucleoprotein (RNP) is a dynamic and multifunctional regulator of RNA Polymerase II (RNAPII) transcription in metazoa. Comprised of the non-coding 7SK RNA, core proteins, and numerous accessory proteins, the most well-known 7SK RNP function is the sequestration and inactivation of the positive transcription elongation factor b (P-TEFb). More recently, 7SK RNP has been shown to regulate RNAPII transcription through P-TEFb-independent pathways. Due to its fundamental role in cellular function, dysregulation has been linked with human diseases including cancers, heart disease, developmental disorders, and viral infection. Significant advances in 7SK RNP structural biology have improved our understanding of 7SK RNP assembly and function. Here, we review progress in understanding the structural basis of 7SK RNA folding, biogenesis, and RNP assembly.
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Affiliation(s)
- Momodou B. Camara
- Department of Chemistry, University of Nebraska, Lincoln, NE, United States
| | - Amr M. Sobeh
- Department of Chemistry, University of Nebraska, Lincoln, NE, United States
| | - Catherine D. Eichhorn
- Department of Chemistry, University of Nebraska, Lincoln, NE, United States
- Nebraska Center for Integrated Biomolecular Communication, Lincoln, NE, United States
- *Correspondence: Catherine D. Eichhorn,
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3
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Shortridge MD, Wille PT, Jones AN, Davidson A, Bogdanovic J, Arts E, Karn J, Robinson JA, Varani G. An ultra-high affinity ligand of HIV-1 TAR reveals the RNA structure recognized by P-TEFb. Nucleic Acids Res 2019; 47:1523-1531. [PMID: 30481318 PMCID: PMC6379670 DOI: 10.1093/nar/gky1197] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/09/2018] [Accepted: 11/23/2018] [Indexed: 12/16/2022] Open
Abstract
The HIV-1 trans-activator protein Tat binds the trans-activation response element (TAR) to facilitate recruitment of the super elongation complex (SEC) to enhance transcription of the integrated pro-viral genome. The Tat–TAR interaction is critical for viral replication and the emergence of the virus from the latent state, therefore, inhibiting this interaction has long been pursued to discover new anti-viral or latency reversal agents. However, discovering active compounds that directly target RNA with high affinity and selectivity remains a significant challenge; limiting pre-clinical development. Here, we report the rational design of a macrocyclic peptide mimic of the arginine rich motif of Tat, which binds to TAR with low pM affinity and 100-fold selectivity against closely homologous RNAs. Despite these unprecedented binding properties, the new ligand (JB181) only moderately inhibits Tat-dependent reactivation in cells and recruitment of positive transcription elongation factor (P-TEFb) to TAR. The NMR structure of the JB181–TAR complex revealed that the ligand induces a structure in the TAR loop that closely mimics the P-TEFb/Tat1:57/AFF4/TAR complex. These results strongly suggest that high-affinity ligands which bind the UCU bulge are not likely to inhibit recruitment of the SEC and suggest that targeting of the TAR loop will be an essential feature of effective Tat inhibitors.
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Affiliation(s)
- Matthew D Shortridge
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700
| | - Paul T Wille
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio 44106-4960
| | - Alisha N Jones
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700
| | - Amy Davidson
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700
| | - Jasmina Bogdanovic
- Department of Chemistry, University of Zurich, Zurich, Switzerland CH-8057
| | - Eric Arts
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio 44106-4960
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, Ohio 44106-4960
| | - John A Robinson
- Department of Chemistry, University of Zurich, Zurich, Switzerland CH-8057
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700
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4
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Desantis J, Massari S, Sosic A, Manfroni G, Cannalire R, Felicetti T, Pannecouque C, Gatto B, Tabarrini O. Design and Synthesis of WM5 Analogues as HIV-1 TAR RNA Binders. THE OPEN MEDICINAL CHEMISTRY JOURNAL 2019. [DOI: 10.2174/1874104501913010016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
The 6-aminoquinolone WM5, previously identified by us, is among the most selective small molecules known as TAR RNA binders to show anti-HIV activity.
Methods:
Starting from WM5, a series of analogues modified at N-1, C-6 or C-7 position was prepared by inserting guanidine or amidine groups as well as other protonable moieties intended to electrostatically bind the phosphate backbone of TAR. All the compounds were tested for their ability to inhibit HIV-1 replication in MT-4 cells and in parallel for their cytotoxicity. The active compounds were also evaluated for their ability to interfere with the formation of the Tat-TAR complex using a Fluorescence Quenching Assay (FQA).
Results:
Some of the synthesized compounds showed an anti-HIV-1 activity in the sub-micromolar range with the naphthyridone derivatives being the most potent. Three of the synthesized derivatives were able to interact with the Tat-TAR complex formation presenting Ki values improved as compared to the values obtained with WM5.
Conclusion:
The addition of a pyridine-based protonable side chain at the N-1 position of the quinolone/naphthyridone core imparted to the compounds the ability to interfere with Tat-TAR complex formation and HIV-1 replication.
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5
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Development of Small Molecules with a Noncanonical Binding Mode to HIV-1 Trans Activation Response (TAR) RNA. J Med Chem 2016; 59:11148-11160. [PMID: 28002966 DOI: 10.1021/acs.jmedchem.6b01450] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Small molecules that bind to RNA potently and specifically are relatively rare. The study of molecules that bind to the HIV-1 transactivation response (TAR) hairpin, a cis-acting HIV genomic element, has long been an important model system for the chemistry of targeting RNA. Here we report the synthesis, biochemical, and structural evaluation of a series of molecules that bind to HIV-1 TAR RNA. A promising analogue, 15, retained the TAR binding affinity of the initial hit and displaced a Tat-derived peptide with an IC50 of 40 μM. NMR characterization of a soluble analogue, 2, revealed a noncanonical binding mode for this class of compounds. Finally, evaluation of 2 and 15 by selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) indicates specificity in binding to TAR within the context of an in vitro-synthesized 365-nt HIV-1 5'-untranslated region (UTR). Thus, these compounds exhibit a novel and specific mode of interaction with TAR, providing important suggestions for RNA ligand design.
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6
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Eichhorn CD, Chug R, Feigon J. hLARP7 C-terminal domain contains an xRRM that binds the 3' hairpin of 7SK RNA. Nucleic Acids Res 2016; 44:9977-9989. [PMID: 27679474 PMCID: PMC5175362 DOI: 10.1093/nar/gkw833] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/02/2016] [Accepted: 09/10/2016] [Indexed: 12/21/2022] Open
Abstract
The 7SK small nuclear ribonucleoprotein (snRNP) sequesters and inactivates the positive transcription elongation factor b (P-TEFb), an essential eukaryotic mRNA transcription factor. The human La-related protein group 7 (hLARP7) is a constitutive component of the 7SK snRNP and localizes to the 3' terminus of the 7SK long noncoding RNA. hLARP7, and in particular its C-terminal domain (CTD), is essential for 7SK RNA stability and assembly with P-TEFb. The hLARP7 N-terminal La module binds and protects the 3' end from degradation, but the structural and functional role of its CTD is unclear. We report the solution NMR structure of the hLARP7 CTD and show that this domain contains an xRRM, a class of atypical RRM first identified in the Tetrahymena thermophila telomerase LARP7 protein p65. The xRRM binds the 3' end of 7SK RNA at the top of stem-loop 4 (SL4) and interacts with both unpaired and base-paired nucleotides. This study confirms that the xRRM is general to the LARP7 family of proteins and defines the binding site for hLARP7 on the 7SK RNA, providing insight into function.
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Affiliation(s)
- Catherine D Eichhorn
- Department of Chemistry and Biochemistry, P.O. Box 951569, University of California, Los Angeles, CA 90095-1569, USA
| | - Rahul Chug
- Department of Chemistry and Biochemistry, P.O. Box 951569, University of California, Los Angeles, CA 90095-1569, USA
| | - Juli Feigon
- Department of Chemistry and Biochemistry, P.O. Box 951569, University of California, Los Angeles, CA 90095-1569, USA
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7
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Krawczyk K, Sim AYL, Knapp B, Deane CM, Minary P. Tertiary Element Interaction in HIV-1 TAR. J Chem Inf Model 2016; 56:1746-54. [DOI: 10.1021/acs.jcim.6b00152] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Konrad Krawczyk
- Department of Computer Science, Oxford University, Parks Road, OX1 3QD Oxford, U.K
| | - Adelene Y. L. Sim
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore, Singapore 138671
| | - Bernhard Knapp
- Department of Statistics, Oxford University, St Giles, OX1 3LB Oxford, U.K
| | - Charlotte M. Deane
- Department of Statistics, Oxford University, St Giles, OX1 3LB Oxford, U.K
| | - Peter Minary
- Department of Computer Science, Oxford University, Parks Road, OX1 3QD Oxford, U.K
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8
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A Phylogenetic Survey on the Structure of the HIV-1 Leader RNA Domain That Encodes the Splice Donor Signal. Viruses 2016; 8:v8070200. [PMID: 27455303 PMCID: PMC4974535 DOI: 10.3390/v8070200] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 06/29/2016] [Accepted: 07/01/2016] [Indexed: 11/16/2022] Open
Abstract
RNA splicing is a critical step in the human immunodeficiency virus type 1 (HIV-1) replication cycle because it controls the expression of the complex viral proteome. The major 5′ splice site (5′ss) that is positioned in the untranslated leader of the HIV-1 RNA transcript is of particular interest because it is used for the production of the more than 40 differentially spliced subgenomic mRNAs. HIV-1 splicing needs to be balanced tightly to ensure the proper levels of all viral proteins, including the Gag-Pol proteins that are translated from the unspliced RNA. We previously presented evidence that the major 5′ss is regulated by a repressive local RNA structure, the splice donor (SD) hairpin, that masks the 11 nucleotides (nts) of the 5′ss signal for recognition by U1 small nuclear RNA (snRNA) of the spliceosome machinery. A strikingly different multiple-hairpin RNA conformation was recently proposed for this part of the HIV-1 leader RNA. We therefore inspected the sequence of natural HIV-1 isolates in search for support, in the form of base pair (bp) co-variations, for the different RNA conformations.
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9
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Belfetmi A, Zargarian L, Tisné C, Sleiman D, Morellet N, Lescop E, Maskri O, René B, Mély Y, Fossé P, Mauffret O. Insights into the mechanisms of RNA secondary structure destabilization by the HIV-1 nucleocapsid protein. RNA (NEW YORK, N.Y.) 2016; 22:506-517. [PMID: 26826129 PMCID: PMC4793207 DOI: 10.1261/rna.054445.115] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 12/06/2015] [Indexed: 06/05/2023]
Abstract
The mature HIV-1 nucleocapsid protein NCp7 (NC) plays a key role in reverse transcription facilitating the two obligatory strand transfers. Several properties contribute to its efficient chaperon activity: preferential binding to single-stranded regions, nucleic acid aggregation, helix destabilization, and rapid dissociation from nucleic acids. However, little is known about the relationships between these different properties, which are complicated by the ability of the protein to recognize particular HIV-1 stem-loops, such as SL1, SL2, and SL3, with high affinity and without destabilizing them. These latter properties are important in the context of genome packaging, during which NC is part of the Gag precursor. We used NMR to investigate destabilization of the full-length TAR (trans activating response element) RNA by NC, which is involved in the first strand transfer step of reverse transcription. NC was used at a low protein:nucleotide (nt) ratio of 1:59 in these experiments. NMR data for the imino protons of TAR identified most of the base pairs destabilized by NC. These base pairs were adjacent to the loops in the upper part of the TAR hairpin rather than randomly distributed. Gel retardation assays showed that conversion from the initial TAR-cTAR complex to the fully annealed form occurred much more slowly at the 1:59 ratio than at the higher ratios classically used. Nevertheless, NC significantly accelerated the formation of the initial complex at a ratio of 1:59.
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Affiliation(s)
- Anissa Belfetmi
- LBPA, ENS de Cachan, CNRS, Université Paris-Saclay, 94235 Cachan Cedex, France
| | - Loussiné Zargarian
- LBPA, ENS de Cachan, CNRS, Université Paris-Saclay, 94235 Cachan Cedex, France
| | - Carine Tisné
- Laboratoire de Cristallographie et RMN biologiques, Université Paris Descartes, CNRS UMR 8015, 75006 Paris Cedex, France
| | - Dona Sleiman
- Laboratoire de Cristallographie et RMN biologiques, Université Paris Descartes, CNRS UMR 8015, 75006 Paris Cedex, France
| | - Nelly Morellet
- Centre de Recherches de Gif, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, 91190 Gif sur Yvette Cedex, France
| | - Ewen Lescop
- Centre de Recherches de Gif, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, 91190 Gif sur Yvette Cedex, France
| | - Ouerdia Maskri
- LBPA, ENS de Cachan, CNRS, Université Paris-Saclay, 94235 Cachan Cedex, France
| | - Brigitte René
- LBPA, ENS de Cachan, CNRS, Université Paris-Saclay, 94235 Cachan Cedex, France
| | - Yves Mély
- Laboratoire de Biophotonique et Pharmacologie, CNRS UMR 7213, Faculté de Pharmacie, Université de Strasbourg, 67401 Illkirch Cedex, France
| | - Philippe Fossé
- LBPA, ENS de Cachan, CNRS, Université Paris-Saclay, 94235 Cachan Cedex, France
| | - Olivier Mauffret
- LBPA, ENS de Cachan, CNRS, Université Paris-Saclay, 94235 Cachan Cedex, France
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10
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Harwig A, Jongejan A, van Kampen AHC, Berkhout B, Das AT. Tat-dependent production of an HIV-1 TAR-encoded miRNA-like small RNA. Nucleic Acids Res 2016; 44:4340-53. [PMID: 26984525 PMCID: PMC4872094 DOI: 10.1093/nar/gkw167] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 03/03/2016] [Indexed: 12/23/2022] Open
Abstract
Evidence is accumulating that retroviruses can produce microRNAs (miRNAs). To prevent cleavage of their RNA genome, retroviruses have to use an alternative RNA source as miRNA precursor. The transacting responsive (TAR) hairpin structure in HIV-1 RNA has been suggested as source for miRNAs, but how these small RNAs are produced without impeding virus replication remained unclear. We used deep sequencing analysis of AGO2-bound HIV-1 RNAs to demonstrate that the 3′ side of the TAR hairpin is processed into a miRNA-like small RNA. This ∼21 nt RNA product is able to repress the expression of mRNAs bearing a complementary target sequence. Analysis of the small RNAs produced by wild-type and mutant HIV-1 variants revealed that non-processive transcription from the HIV-1 LTR promoter results in the production of short TAR RNAs that serve as precursor. These TAR RNAs are cleaved by Dicer and processing is stimulated by the viral Tat protein. This biogenesis pathway differs from the canonical miRNA pathway and allows HIV-1 to produce the TAR-encoded miRNA-like molecule without cleavage of the RNA genome.
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Affiliation(s)
- Alex Harwig
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Aldo Jongejan
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Antoine H C van Kampen
- Bioinformatics Laboratory, Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Atze T Das
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
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11
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Castro SI, Hleap JS, Cárdenas H, Blouin C. Molecular organization of the 5S rDNA gene type II in elasmobranchs. RNA Biol 2015; 13:391-9. [PMID: 26488198 PMCID: PMC4841605 DOI: 10.1080/15476286.2015.1100796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 09/21/2015] [Indexed: 10/22/2022] Open
Abstract
The 5S rDNA gene is a non-coding RNA that can be found in 2 copies (type I and type II) in bony and cartilaginous fish. Previous studies have pointed out that type II gene is a paralog derived from type I. We analyzed the molecular organization of 5S rDNA type II in elasmobranchs. Although the structure of the 5S rDNA is supposed to be highly conserved, our results show that the secondary structure in this group possesses some variability and is different than the consensus secondary structure. One of these differences in Selachii is an internal loop at nucleotides 7 and 112. These mutations observed in the transcribed region suggest an independent origin of the gene among Batoids and Selachii. All promoters were highly conserved with the exception of BoxA, possibly due to its affinity to polymerase III. This latter enzyme recognizes a dT4 sequence as stop signal, however in Rajiformes this signal was doubled in length to dT8. This could be an adaptation toward a higher efficiency in the termination process. Our results suggest that there is no TATA box in elasmobranchs in the NTS region. We also provide some evidence suggesting that the complexity of the microsatellites present in the NTS region play an important role in the 5S rRNA gene since it is significantly correlated with the length of the NTS.
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Affiliation(s)
- Sergio I. Castro
- Grupo de Estudios en Genética Ecología Molecular y Fisiología Animal, Universidad del Valle, Cali, Colombia
- Fundación Colombiana para la Investigación y Conservación de Tiburones y Rayas, SQUALUS. Cali, Colombia
| | - Jose S. Hleap
- Grupo de Estudios en Genética Ecología Molecular y Fisiología Animal, Universidad del Valle, Cali, Colombia
- Fundación Colombiana para la Investigación y Conservación de Tiburones y Rayas, SQUALUS. Cali, Colombia
- Canadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Heiber Cárdenas
- Grupo de Estudios en Genética Ecología Molecular y Fisiología Animal, Universidad del Valle, Cali, Colombia
| | - Christian Blouin
- Canadian Institute for Advanced Research, Program in Evolutionary Biology, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Department of Computer Science, Dalhousie University, Halifax, Canada
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12
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Strom S, Shiskova E, Hahm Y, Grover N. Thermodynamic examination of 1- to 5-nt purine bulge loops in RNA and DNA constructs. RNA (NEW YORK, N.Y.) 2015; 21:1313-22. [PMID: 26022248 PMCID: PMC4478350 DOI: 10.1261/rna.046631.114] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 04/09/2015] [Indexed: 05/24/2023]
Abstract
Bulge loops are common features of RNA structures that are involved in the formation of RNA tertiary structures and are often sites for interactions with proteins and ions. Minimal thermodynamic data currently exist on the bulge size and sequence effects. Using thermal denaturation methods, thermodynamic properties of 1- to 5-nt adenine and guanine bulge loop constructs were examined in 10 mM MgCl(2) or 1 M KCl. The [Formula: see text] loop parameters for 1- to 5-nt purine bulge loops in RNA constructs were between 3.07 and 5.31 kcal/mol in 1 M KCl buffer. In 10 mM magnesium ions, the ΔΔG° values relative to 1 M KCl were 0.47-2.06 kcal/mol more favorable for the RNA bulge loops. The [Formula: see text] loop parameters for 1- to 5-nt purine bulge loops in DNA constructs were between 4.54 and 5.89 kcal/mol. Only 4- and 5-nt guanine constructs showed significant change in stability for the DNA constructs in magnesium ions. A linear correlation is seen between the size of the bulge loop and its stability. New prediction models are proposed for 1- to 5-nt purine bulge loops in RNA and DNA in 1 M KCl. We show that a significant stabilization is seen for small bulge loops in RNA in the presence of magnesium ions. A prediction model is also proposed for 1- to 5-nt purine bulge loop RNA constructs in 10 mM magnesium chloride.
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Affiliation(s)
- Shane Strom
- Department of Chemistry and Biochemistry, Colorado College, Colorado Springs, Colorado 80903, USA
| | - Evgenia Shiskova
- Department of Chemistry and Biochemistry, Colorado College, Colorado Springs, Colorado 80903, USA
| | - Yaeeun Hahm
- Department of Chemistry and Biochemistry, Colorado College, Colorado Springs, Colorado 80903, USA
| | - Neena Grover
- Department of Chemistry and Biochemistry, Colorado College, Colorado Springs, Colorado 80903, USA
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13
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Fonseca R, Pachov DV, Bernauer J, van den Bedem H. Characterizing RNA ensembles from NMR data with kinematic models. Nucleic Acids Res 2014; 42:9562-72. [PMID: 25114056 PMCID: PMC4150802 DOI: 10.1093/nar/gku707] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Revised: 07/18/2014] [Accepted: 07/21/2014] [Indexed: 12/03/2022] Open
Abstract
Functional mechanisms of biomolecules often manifest themselves precisely in transient conformational substates. Researchers have long sought to structurally characterize dynamic processes in non-coding RNA, combining experimental data with computer algorithms. However, adequate exploration of conformational space for these highly dynamic molecules, starting from static crystal structures, remains challenging. Here, we report a new conformational sampling procedure, KGSrna, which can efficiently probe the native ensemble of RNA molecules in solution. We found that KGSrna ensembles accurately represent the conformational landscapes of 3D RNA encoded by NMR proton chemical shifts. KGSrna resolves motionally averaged NMR data into structural contributions; when coupled with residual dipolar coupling data, a KGSrna ensemble revealed a previously uncharacterized transient excited state of the HIV-1 trans-activation response element stem-loop. Ensemble-based interpretations of averaged data can aid in formulating and testing dynamic, motion-based hypotheses of functional mechanisms in RNAs with broad implications for RNA engineering and therapeutic intervention.
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Affiliation(s)
- Rasmus Fonseca
- AMIB Project, INRIA Saclay-Île de France, 1 rue Honoré d'Estienne d'Orves, Bâtiment Alan Turing, Campus de l'École Polytechnique, 91120 Palaiseau, France Laboratoire d'Informatique de l'École Polytechnique (LIX), CNRS UMR 7161, École Polytechnique, 91128 Palaiseau, France Department of Computer Science, University of Copenhagen, Nørre Campus, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Dimitar V Pachov
- Department of Chemistry, Stanford University, 333 Campus Dr., Stanford, CA 94305, USA
| | - Julie Bernauer
- AMIB Project, INRIA Saclay-Île de France, 1 rue Honoré d'Estienne d'Orves, Bâtiment Alan Turing, Campus de l'École Polytechnique, 91120 Palaiseau, France Laboratoire d'Informatique de l'École Polytechnique (LIX), CNRS UMR 7161, École Polytechnique, 91128 Palaiseau, France
| | - Henry van den Bedem
- Joint Center for Structural Genomics, Stanford Synchrotron Radiation Lightsource, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
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14
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Kuzembayeva M, Dilley K, Sardo L, Hu WS. Life of psi: how full-length HIV-1 RNAs become packaged genomes in the viral particles. Virology 2014; 454-455:362-70. [PMID: 24530126 DOI: 10.1016/j.virol.2014.01.019] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 01/03/2014] [Accepted: 01/24/2014] [Indexed: 12/27/2022]
Abstract
As a member of the retrovirus family, HIV-1 packages its RNA genome into particles and replicates through a DNA intermediate that integrates into the host cellular genome. The multiple genes encoded by HIV-1 are expressed from the same promoter and their expression is regulated by splicing and ribosomal frameshift. The full-length HIV-1 RNA plays a central role in viral replication as it serves as the genome in the progeny virus and is used as the template for Gag and GagPol translation. In this review, we summarize findings that contribute to our current understanding of how full-length RNA is expressed and transported, cis- and trans-acting elements important for RNA packaging, the locations and timing of RNA:RNA and RNA:Gag interactions, and the processes required for this RNA to be packaged into viral particles.
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Affiliation(s)
- Malika Kuzembayeva
- Viral Recombination Section, HIV Drug Resistance Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Kari Dilley
- Viral Recombination Section, HIV Drug Resistance Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Luca Sardo
- Viral Recombination Section, HIV Drug Resistance Program, National Cancer Institute, Frederick, MD 21702, USA
| | - Wei-Shau Hu
- Viral Recombination Section, HIV Drug Resistance Program, National Cancer Institute, Frederick, MD 21702, USA.
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15
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Eilebrecht S, Wilhelm E, Benecke BJ, Bell B, Benecke AG. HMGA1 directly interacts with TAR to modulate basal and Tat-dependent HIV transcription. RNA Biol 2013; 10:436-44. [PMID: 23392246 DOI: 10.4161/rna.23686] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The transactivating response element (TAR) of human immunodeficiency virus 1 (HIV-1) is essential for promoter transactivation by the viral transactivator of transcription (Tat). The Tat-TAR interaction thereby recruits active positive transcription elongation factor b (P-TEFb) from its inactive, 7SK/HEXIM1-bound form, leading to efficient viral transcription. Here, we show that the 7SK RNA-associating chromatin regulator HMGA1 can specifically bind to the HIV-1 TAR element and that 7SK RNA can thereby compete with TAR. The HMGA1-binding interface of TAR is located within the binding site for Tat and other cellular activators, and we further provide evidence for competition between HMGA1 and Tat for TAR-binding. HMGA1 negatively influences the expression of a HIV-1 promoter-driven reporter in a TAR-dependent manner, both in the presence and in the absence of Tat. The overexpression of the HMGA1-binding substructure of 7SK RNA results in a TAR-dependent gain of HIV-1 promoter activity similar to the effect of the shRNA-mediated knockdown of HMGA1. Our results support a model in which the HMGA1/TAR interaction prevents the binding of transcription-activating cellular co-factors and Tat, subsequently leading to reduced HIV-1 transcription.
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Affiliation(s)
- Sebastian Eilebrecht
- Institut des Hautes Études Scientifiques - Centre National de la Recherche Scientifique; Bures sur Yvette; France & Vaccine Research Institute; Institut Mondor de Recherche Biomédicale; Créteil, France
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16
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Jeong HS, Kang S, Lee JY, Kim BH. Probing specific RNA bulge conformations by modified fluorescent nucleosides. Org Biomol Chem 2009; 7:921-5. [DOI: 10.1039/b816768k] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Characterizing complex dynamics in the transactivation response element apical loop and motional correlations with the bulge by NMR, molecular dynamics, and mutagenesis. Biophys J 2008; 95:3906-15. [PMID: 18621815 DOI: 10.1529/biophysj.108.140285] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The HIV-1 transactivation response element (TAR) RNA binds a variety of proteins and is a target for developing anti-HIV therapies. TAR has two primary binding sites: a UCU bulge and a CUGGGA apical loop. We used NMR residual dipolar couplings, carbon spin relaxation (R(1) and R(2)), and relaxation dispersion (R(1rho)) in conjunction with molecular dynamics and mutagenesis to characterize the dynamics of the TAR apical loop and investigate previously proposed long-range interactions with the distant bulge. Replacement of the wild-type apical loop with a UUCG loop did not significantly affect the structural dynamics at the bulge, indicating that the apical loop and the bulge act largely as independent dynamical recognition centers. The apical loop undergoes complex dynamics at multiple timescales that are likely important for adaptive recognition: U31 and G33 undergo limited motions, G32 is highly flexible at picosecond-nanosecond timescales, and G34 and C30 form a dynamic Watson-Crick basepair in which G34 and A35 undergo a slow (approximately 30 mus) likely concerted looping in and out motion, with A35 also undergoing large amplitude motions at picosecond-nanosecond timescales. Our study highlights the power of combining NMR, molecular dynamics, and mutagenesis in characterizing RNA dynamics.
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18
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Vieregg J, Cheng W, Bustamante C, Tinoco I. Measurement of the effect of monovalent cations on RNA hairpin stability. J Am Chem Soc 2007; 129:14966-73. [PMID: 17997555 DOI: 10.1021/ja074809o] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Using optical tweezers, we have measured the effect of monovalent cation concentration and species on the folding free energy of five large (49-124 nt) RNA hairpins, including HIV-1 TAR and molecules approximating A.U and G.C homopolymers. RNA secondary structure thermodynamics are accurately described by a model consisting of nearest-neighbor interactions and additive loop and bulge terms. Melting of small (<15 bp) duplexes and hairpins in 1 M NaCl has been used to determine the parameters of this model, which is now used extensively to predict structure and folding dynamics. Few systematic measurements have been made in other ionic conditions or for larger structures. By applying mechanical force, we measured the work required to fold and unfold single hairpins at room temperature over a range of cation concentrations from 50 to 1000 mM. Free energies were then determined using the Crooks fluctuation theorem. We observed the following: (1) In most cases, the nearest-neighbor model accurately predicted the free energy of folding at 1 M NaCl. (2) Free energy was proportional to the logarithm of salt concentration. (3) Substituting potassium ions for sodium slightly decreased hairpin stability. The TAR hairpin also misfolded nearly twice as often in KCl, indicating a differential kinetic response. (4) Monovalent cation concentration affects RNA stability in a sequence-dependent manner. G.C helices were unaffected by changing salt concentration, A.U helices were modestly affected, and the hairpin loop was very sensitive. Surprisingly, the U.C.U bulge of TAR was found to be equally stable in all conditions tested. We also report a new estimate for the elastic parameters of single-stranded RNA.
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Affiliation(s)
- Jeffrey Vieregg
- Department of Physics, University of California, Berkeley, California 94720, USA.
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19
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Musselman C, Al-Hashimi HM, Andricioaei I. iRED analysis of TAR RNA reveals motional coupling, long-range correlations, and a dynamical hinge. Biophys J 2007; 93:411-22. [PMID: 17449677 PMCID: PMC1896250 DOI: 10.1529/biophysj.107.104620] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The HIV-1 transactivation response RNA element (TAR), which is essential to the lifecycle of the virus, has been suggested, based on NMR and hydrodynamic measurements, to undergo substantial, collective, structural dynamics that are important for its function. To deal with the significant coupling between overall diffusional rotation and internal motion expected to exist in TAR, here we utilize an isotropic reorientational eigenmode dynamics analysis of simulated molecular trajectories to obtain a detailed description of TAR dynamics and an accurately quantified pattern of dynamical correlations. The analysis demonstrates the inseparability of internal and overall motional modes, confirms the existence and reveals the nature of collective domain dynamics, and additionally reveals that the hinge for these motions is centered on residues U23, C24, and C41. Results also indicate the existence of long-range communication between the loop and the core of the RNA, and between the loop and the bulge. Additionally, the isotropic reorientational eigenmode dynamics analysis explains, from a dynamical perspective, several existing biochemical mutational studies and suggests new mutations for future structural dynamics studies.
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Affiliation(s)
- Catherine Musselman
- Department of Chemistry and The Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, Michigan, USA
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20
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Girard FC, Ottink OM, Ampt KA, Tessari M, Wijmenga SS. Thermodynamics and NMR studies on Duck, Heron and Human HBV encapsidation signals. Nucleic Acids Res 2007; 35:2800-11. [PMID: 17430968 PMCID: PMC1885660 DOI: 10.1093/nar/gkm131] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Hepatitis B virus (HBV) replication is initiated by binding of its reverse transcriptase (P) to the apical stem-loop (AL) and primer loop (PL) of epsilon, a highly conserved RNA element at the 5'-end of the RNA pregenome. Mutation studies on duck/heron and human in vitro systems have shown similarities but also differences between their P-epsilon interaction. Here, NMR and UV thermodynamic data on AL (and PL) from these three species are presented. The stabilities of the duck and heron ALs were found to be similar, and much lower than that of human. NMR data show that this low stability stems from an 11-nt internal bulge destabilizing the stem of heron AL. In duck, although structured at low temperature, this region also forms a weak point as its imino resonances broaden to disappearance between 30 and 35 degrees C well below the overall AL melting temperature. Surprisingly, the duck- and heron ALs were both found to be capped by a stable well-structured UGUU tetraloop. All avian ALs are expected to adhere to this because of their conserved sequence. Duck PL is stable and structured and, in view of sequence similarities, the same is expected for heron - and human PL.
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Affiliation(s)
| | | | | | | | - Sybren S. Wijmenga
- *To whom correspondence should be addressed +31 24 3653384/2678+31 24 3652112
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21
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Nagy G, Ward J, Mosser DD, Koncz A, Gergely P, Stancato C, Qian Y, Fernandez D, Niland B, Grossman CE, Telarico T, Banki K, Perl A. Regulation of CD4 expression via recycling by HRES-1/RAB4 controls susceptibility to HIV infection. J Biol Chem 2006; 281:34574-91. [PMID: 16935861 DOI: 10.1074/jbc.m606301200] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A novel 2986-base transcript encoded by the antisense strand of the HRES-1 human endogenous retrovirus was isolated from peripheral blood lymphocytes. This transcript codes for a 218-amino acid protein, termed HRES-1/Rab4, based on homology to the Rab4 family of small GTPases. Antibody 13407 raised against recombinant HRES-1/Rab4 detected a native protein of identical molecular weight in human T cells. HRES-1 nucleotides 2151-1606, located upstream of HRES-1/Rab4 exon 1, have promoter activity when oriented in the direction of HRES-1/Rab4 transcription. The human immunodeficiency virus, type 1 (HIV-1), tat gene stimulates transcriptional activity of the HRES-1/Rab4 promoter via trans-activation of the HRES-1 long terminal repeat. Transfection of HIV-1 tat into HeLa cells or infection of H9 and Jurkat cells by HIV-1 increased HRES-1/Rab4 protein levels. Overexpression of HRES-1/Rab4 in Jurkat cells abrogated HIV infection, gag p24 production, and apoptosis, whereas dominant-negative HRES-1/Rab4(S27N) had the opposite effects. HRES-1/Rab4 inhibited surface expression of CD4 and targeted it for lysosomal degradation. HRES-1/Rab4(S27N) enhanced surface expression, recycling, and total cellular CD4 content. Infection by HIV elicited a coordinate down-regulation of CD4 and up-regulation of HRES-1/Rab4 in PBL. Moreover, overexpression of HRES-1/Rab4 reduced CD4 expression on peripheral blood CD4+ T cells. Stimulation by HIV-1 of HRES-1/Rab4 expression and its regulation of CD4 recycling reveal novel coordinate interactions between an infectious retrovirus and the human genome.
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Affiliation(s)
- Gyorgy Nagy
- Department of Medicine, State University of New York, College of Medicine, Syracuse, New York 13210, USA
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22
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Xiao Z, Zhang N, Lin Y, Jones GB, Goldberg IH. Spirocyclic helical compounds as binding agents for bulged RNA, including HIV-2 TAR. Chem Commun (Camb) 2006:4431-3. [PMID: 17057867 DOI: 10.1039/b610007d] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Based on fluorescence binding studies and 1D 1H NMR studies, designed synthetic analogues of NCSi-gb bind specifically with two-base bulged RNA, including HIV-2 TAR RNA, making them potential lead compounds for antiviral drug development.
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Affiliation(s)
- Ziwei Xiao
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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23
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Paillart JC, Dettenhofer M, Yu XF, Ehresmann C, Ehresmann B, Marquet R. First snapshots of the HIV-1 RNA structure in infected cells and in virions. J Biol Chem 2004; 279:48397-403. [PMID: 15355993 DOI: 10.1074/jbc.m408294200] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
With the increasing interest of RNAs in regulating a range of cell biological processes, very little is known about the structure of RNAs in tissue culture cells. We focused on the 5'-untranslated region of the human immunodeficiency virus type 1 RNA genome, a highly conserved RNA region, which contains structural domains that regulate key steps in the viral replication cycle. Up until now, structural information only came from in vitro studies. Here, we developed chemical modification assays to test nucleotide accessibility directly in infected cells and viral particles, thus circumventing possible biases and artifacts linked to in vitro assays. The secondary structure of the 5'-untranslated region in infected cells points to the existence of the various stem-loop motifs associated to distinct functions, proposed from in vitro probing, mutagenesis, and phylogeny. However, compared with in vitro data, subtle differences were observed in the dimerization initiation site hairpin, and none of the proposed long range interactions were observed between the functional domains. Moreover, no global RNA rearrangement was observed; structural differences between infected cells and viral particles were limited to the primer binding site, which became protected against chemical modification upon tRNA(3) (Lys) annealing in virions and to the main packaging signal. In addition, our data suggested that the genomic RNA could already dimerize in the cytoplasm of infected cells. Taken together, our results provided the first analysis of the dynamic of RNA structure of the human immunodeficiency virus type 1 RNA genome during virus assembly ex vivo.
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Affiliation(s)
- Jean-Christophe Paillart
- Unité Propre de Recherche 9002 du CNRS conventionnée à l'Université Louis Pasteur, Institut de Biologie Moléculaire et Cellulaire, 15 rue René Descartes, 67084 Strasbourg cedex, France.
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