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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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Zhao S, Cui H, Hu Z, Du L, Ran X, Wen X. Senecavirus A Enhances Its Adaptive Evolution via Synonymous Codon Bias Evolution. Viruses 2022; 14:v14051055. [PMID: 35632797 PMCID: PMC9146685 DOI: 10.3390/v14051055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 12/10/2022] Open
Abstract
Synonymous codon bias in the viral genome affects protein translation and gene expression, suggesting that the synonymous codon mutant plays an essential role in influencing virulence and evolution. However, how the recessive mutant form contributes to virus evolvability remains elusive. In this paper, we characterize how the Senecavirus A (SVA), a picornavirus, utilizes synonymous codon mutations to influence its evolution, resulting in the adaptive evolution of the virus to adverse environments. The phylogenetic tree and Median-joining (MJ)-Network of these SVA lineages worldwide were constructed to reveal SVA three-stage genetic development clusters. Furthermore, we analyzed the codon bias of the SVA genome of selected strains and found that SVA could increase the GC content of the third base of some amino acid synonymous codons to enhance the viral RNA adaptive evolution. Our results highlight the impact of recessive mutation of virus codon bias on the evolution of the SVA and uncover a previously underappreciated evolutionary strategy for SVA. They also underline the importance of understanding the genetic evolution of SVA and how SVA adapts to the adverse effects of external stress.
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Affiliation(s)
- Simiao Zhao
- College of Animal Science and Technology, Hainan University, Haikou 570228, China; (S.Z.); (H.C.); (Z.H.); (L.D.)
| | - Huiqi Cui
- College of Animal Science and Technology, Hainan University, Haikou 570228, China; (S.Z.); (H.C.); (Z.H.); (L.D.)
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhenru Hu
- College of Animal Science and Technology, Hainan University, Haikou 570228, China; (S.Z.); (H.C.); (Z.H.); (L.D.)
| | - Li Du
- College of Animal Science and Technology, Hainan University, Haikou 570228, China; (S.Z.); (H.C.); (Z.H.); (L.D.)
| | - Xuhua Ran
- College of Animal Science and Technology, Hainan University, Haikou 570228, China; (S.Z.); (H.C.); (Z.H.); (L.D.)
- Correspondence: (X.R.); (X.W.)
| | - Xiaobo Wen
- College of Animal Science and Technology, Hainan University, Haikou 570228, China; (S.Z.); (H.C.); (Z.H.); (L.D.)
- Correspondence: (X.R.); (X.W.)
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Azéma L, Bonnet-Salomon S, Endo M, Takeuchi Y, Durand G, Emura T, Hidaka K, Dausse E, Sugiyama H, Toulmé JJ. Triggering nucleic acid nanostructure assembly by conditional kissing interactions. Nucleic Acids Res 2019; 46:1052-1058. [PMID: 29272518 PMCID: PMC5814900 DOI: 10.1093/nar/gkx1267] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 12/07/2017] [Indexed: 02/07/2023] Open
Abstract
Nucleic acids are biomolecules of amazing versatility. Beyond their function for information storage they can be used for building nano-objects. We took advantage of loop–loop or kissing interactions between hairpin building blocks displaying complementary loops for driving the assembly of nucleic acid nano-architectures. It is of interest to make the interaction between elementary units dependent on an external trigger, thus allowing the control of the scaffold formation. To this end we exploited the binding properties of structure-switching aptamers (aptaswitch). Aptaswitches are stem–loop structured oligonucleotides that engage a kissing complex with an RNA hairpin in response to ligand-induced aptaswitch folding. We demonstrated the potential of this approach by conditionally assembling oligonucleotide nanorods in response to the addition of adenosine.
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Affiliation(s)
- Laurent Azéma
- University of Bordeaux, CNRS UMR 5320, INSERM U1212, Bordeaux 33076, France
| | | | - Masayuki Endo
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.,Institute for Integrated Cell-Material Science, Kyoto University, Kyoto 606-8501, Japan
| | - Yosuke Takeuchi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Guillaume Durand
- University of Bordeaux, CNRS UMR 5320, INSERM U1212, Bordeaux 33076, France
| | - Tomoko Emura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Eric Dausse
- University of Bordeaux, CNRS UMR 5320, INSERM U1212, Bordeaux 33076, France
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.,Institute for Integrated Cell-Material Science, Kyoto University, Kyoto 606-8501, Japan
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