Genome sequence analysis suggests coevolution of the DIS, SD, and Psi hairpins in HIV-1 genomes
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. Despit...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-11-01
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| Series: | Virus Research |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S0168170222002386 |
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| author | Margarita.I. Zarudnaya Andriy.L. Potyahaylo Iryna.M. Kolomiets Leonid.G. Gorb |
| author_facet | Margarita.I. Zarudnaya Andriy.L. Potyahaylo Iryna.M. Kolomiets Leonid.G. Gorb |
| author_sort | Margarita.I. Zarudnaya |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-08T17:06:49Z |
| format | Article |
| id | doaj.art-5c1c5896efa949d194ac8e4d2c3fbf40 |
| institution | Directory Open Access Journal |
| issn | 1872-7492 |
| language | English |
| last_indexed | 2024-03-08T17:06:49Z |
| publishDate | 2022-11-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Virus Research |
| spelling | doaj.art-5c1c5896efa949d194ac8e4d2c3fbf402024-01-04T04:36:07ZengElsevierVirus Research1872-74922022-11-01321198910Genome sequence analysis suggests coevolution of the DIS, SD, and Psi hairpins in HIV-1 genomesMargarita.I. Zarudnaya0Andriy.L. Potyahaylo1Iryna.M. Kolomiets2Leonid.G. Gorb3Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Akademika Zabolotnoho Str, Kyiv 03143, UkraineDepartment of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Akademika Zabolotnoho Str, Kyiv 03143, UkraineDepartment of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Akademika Zabolotnoho Str, Kyiv 03143, UkraineCorresponding author.; Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Akademika Zabolotnoho Str, Kyiv 03143, UkraineHIV-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.http://www.sciencedirect.com/science/article/pii/S0168170222002386HIV-1 M groupPhylogenetic analysisRNA secondary structureDIS hairpinSD hairpinPsi hairpin |
| spellingShingle | Margarita.I. Zarudnaya Andriy.L. Potyahaylo Iryna.M. Kolomiets Leonid.G. Gorb Genome sequence analysis suggests coevolution of the DIS, SD, and Psi hairpins in HIV-1 genomes Virus Research HIV-1 M group Phylogenetic analysis RNA secondary structure DIS hairpin SD hairpin Psi hairpin |
| title | Genome sequence analysis suggests coevolution of the DIS, SD, and Psi hairpins in HIV-1 genomes |
| title_full | Genome sequence analysis suggests coevolution of the DIS, SD, and Psi hairpins in HIV-1 genomes |
| title_fullStr | Genome sequence analysis suggests coevolution of the DIS, SD, and Psi hairpins in HIV-1 genomes |
| title_full_unstemmed | Genome sequence analysis suggests coevolution of the DIS, SD, and Psi hairpins in HIV-1 genomes |
| title_short | Genome sequence analysis suggests coevolution of the DIS, SD, and Psi hairpins in HIV-1 genomes |
| title_sort | genome sequence analysis suggests coevolution of the dis sd and psi hairpins in hiv 1 genomes |
| topic | HIV-1 M group Phylogenetic analysis RNA secondary structure DIS hairpin SD hairpin Psi hairpin |
| url | http://www.sciencedirect.com/science/article/pii/S0168170222002386 |
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