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Zarudnaya MI, Potyahaylo AL, Kolomiets IM, Gorb LG. Structural diversity of the region encompassing DIS, SD and Psi hairpins in HIV and SIV genomes. Virus Res 2023; 336:199197. [PMID: 37574135 PMCID: PMC10483063 DOI: 10.1016/j.virusres.2023.199197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/15/2023]
Abstract
We investigated in silico the secondary structure of the region encompassing DIS, SD and Psi hairpins in HIV-1 genomes of rare groups N, O and P, HIV-2 genomes and SIV genomes from chimpanzees, gorillas and monkeys. We found that the structure of this region in SIVcpzptt genomes of the 1st and the 2nd clusters is similar to that in HIV-1 genomes of groups M and N, respectively. Further, the structure of the region encompassing DIS, SD and Psi hairpins is similar in HIV-1 genomes of groups O and P and SIVgor genomes. Here we report that the DIS hairpin and truncated Psi hairpin are conserved in all HIV-1 and SIVcpz/gor genomes studied, while only the sequence of the splice donor site, but not the architecture of the SD hairpin involving this signal is conserved in HIV-1N/O/P and SIVcpz/gor genomes. A study on the 5' leader structure in genomes of 28 different SIV lineages infecting monkeys showed that the domain closed by U5-AUG duplex can form in all these genomes. This domain mainly consists of 2 subdomains, one of which includes the signal PBS (PBS subdomain) and another contains a putative DIS hairpin (DIS subdomain). DIS subdomains contain 1-8 hairpins. None of them is similar to those in HIV-1 or SIVcpz/gor genomes. The palindrome GUGCAC was found only in SIVdrl/mnd-2, the GACGC-GCGUC duplex (Sakuragi et al., 2012) - only in SIVrcm/drl/mnd-2 and a putative 5' G-quadruplex - in SIVdeb/drl/rcm/stm genomes. In genomes of eight SIV lineages, DIS hairpin has palindrome UGCGCA. Studies on the 5' leader in 64 HIV-2 genomes of different subtypes showed, in particular, that this region has sequences of a putative 5' G-quadruplex and a putative duplex similar to the GACGC-GCGUC duplex. The secondary structures of the region encompassing DIS, SD and Psi hairpins in HIV-2 genomes of subtype B and recombinant 01_AB are similar and differ from that in genomes of subtype A.
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Affiliation(s)
- M I Zarudnaya
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv, 03143, Ukraine
| | - A L Potyahaylo
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv, 03143, Ukraine
| | - I M Kolomiets
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv, 03143, Ukraine
| | - L G Gorb
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150, Akademika Zabolotnoho Str., Kyiv, 03143, Ukraine.
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Zarudnaya MI, Potyahaylo AL, Kolomiets IM, Gorb LG. Genome sequence analysis suggests coevolution of the DIS, SD, and Psi hairpins in HIV-1 genomes. Virus Res 2022; 321:198910. [PMID: 36070810 DOI: 10.1016/j.virusres.2022.198910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 08/28/2022] [Accepted: 08/31/2022] [Indexed: 12/24/2022]
Abstract
HIV-1 RNA dimerization is a critical step in viral life cycle. It is a prerequisite for genome packaging and plays an important role in reverse transcription and recombination. Dimerization is promoted by the DIS (dimerization initiation site) hairpin located in the 5' leader of HIV-1 genome. Despite the high genetic diversity in HIV-1 group M, only five apical loops (AAGCGCGCA, AAGUGCGCA, AAGUGCACA, AGGUGCACA and AGUGCAC) are commonly found in DIS hairpins. We refer to the parent DISes with these apical loops as DISLai, DISTrans, DISF, DISMal, and DISC, respectively. Based on identity or similarity of DIS hairpins to parent DISes, we distributed HIV-1 M genomes into five dimerization groups. Comparison of the primary and secondary structures of DIS, SD and Psi hairpins in about 3000 HIV-1 M genomes showed that the mutation frequencies at particular nucleotide positions of these hairpins differ among the dimerization groups, and DISF may be an origin of other parent DISes. We found that DIS, SD and Psi hairpins have hundreds of variants, only some of them occurring rather frequently. The lower part of DIS hairpin with G x AGG internal loop is highly conserved in both HIV-1 and SIV genomes. We supposed that the G-quadruplex, located 56 nts downstream of the Gag start codon, may participate in switching of HIV-1 leader RNA from BMH (branched multiple hairpins) to LDI (long distance interaction) conformation.
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Affiliation(s)
- Margarita I Zarudnaya
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Akademika Zabolotnoho Str, Kyiv 03143, Ukraine
| | - Andriy L Potyahaylo
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Akademika Zabolotnoho Str, Kyiv 03143, Ukraine
| | - Iryna M Kolomiets
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Akademika Zabolotnoho Str, Kyiv 03143, Ukraine
| | - Leonid G Gorb
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Akademika Zabolotnoho Str, Kyiv 03143, Ukraine.
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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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Herrera-Carrillo E, Berkhout B. Potential mechanisms for cell-based gene therapy to treat HIV/AIDS. Expert Opin Ther Targets 2014; 19:245-63. [PMID: 25388088 DOI: 10.1517/14728222.2014.980236] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION An estimated 35 million people are infected with HIV worldwide. Anti-retroviral therapy (ART) has reduced the morbidity and mortality of HIV-infected patients but efficacy requires strict adherence and the treatment is not curative. Most importantly, the emergence of drug-resistant virus strains and drug toxicity can restrict the long-term therapeutic efficacy in some patients. Therefore, novel treatment strategies that permanently control or eliminate the virus and restore the damaged immune system are required. Gene therapy against HIV infection has been the topic of intense investigations for the last two decades because it can theoretically provide such a durable anti-HIV control. AREAS COVERED In this review we discuss two major gene therapy strategies to combat HIV. One approach aims to kill HIV-infected cells and the other is based on the protection of cells from HIV infection. We discuss the underlying molecular mechanisms for candidate approaches to permanently block HIV infection, including the latest strategies and future therapeutic applications. EXPERT OPINION Hematopoietic stem cell-based gene therapy for HIV/AIDS may eventually become an alternative for standard ART and should ideally provide a functional cure in which the virus is durably controlled without medication. Recent results from preclinical research and early-stage clinical trials support the feasibility and safety of this novel strategy.
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Affiliation(s)
- Elena Herrera-Carrillo
- Academic Medical Center University of Amsterdam, Department of Medical Microbiology , Meibergdreef 15, Amsterdam, 1105 AZ , The Netherlands
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