Analysis of HIV-1 (Human immunodeficiency virus-1, Lentivirus, Orthoretrovirinae, Retroviridae) Nef protein polymorphism of variants circulating in the former USSR countries

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Abstract

Introduction. The human immunodeficiency virus (HIV) Nef protein is one of the key factors determining the infectivity and replicative properties of HIV. With the ability to interact with numerous proteins of the host cell, this protein provides the maximum level of virus production and protects it from the immune system. The main activities of Nef are associated with a decrease in the expression of the CD4 receptor and major histocompatibility complex class I molecules (MHC-I), as well as the rearrangement of the cytoskeleton. These properties of the protein are determined by the structure of several motifs in the structure of the nef gene encoding it, which is quite variable.
Goals and tasks. The main goal of the work was to analyze the characteristics of Nef protein of HIV-1 variant A6, which dominates in the countries of the former USSR. The objective of the work was a comparative analysis of natural polymorphisms in the nef gene of HIV-1 sub-subtypes A6 and A1 and subtype B.
Material and methods. The sequences of the HIV-1 genome obtained during the previous work of the laboratory were used, as well as the reference sequence from GenBank. In this work, Sanger sequencing and new generation sequencing methods, as well as bioinformation analysis methods were used.
Results and discussion. The existence of noticeable differences in the prevalence of Nef natural polymorphisms (A32P, E38D, I43V, A54D, Q104K, H116N, Y120F, Y143F, V168M, H192T, V194R, R35Q, D108E, Y135F, E155K, E182M, R184K and F191L), some of which are characteristic mutations for variant A6, was shown. Conclusion. Characteristic substitutions were found in the Nef structure, potentially capable of weakening the replicative properties of HIV-1 variant A6.

About the authors

K. B. Gromov

National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya

Email: fake@neicon.ru
ORCID iD: 0000-0002-9316-1975
Moscow, 123098 Россия

E. V. Kazennova

National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya

Email: fake@neicon.ru
ORCID iD: 0000-0002-7896-2379
Moscow, 123098 Россия

D. E. Kireev

Central Research Institute of Epidemiology

Email: fake@neicon.ru
ORCID iD: 0000-0002-1390-8021
Moscow, 111123 Россия

A. V. Murzakova

Central Research Institute of Epidemiology

Email: fake@neicon.ru
ORCID iD: 0000-0002-2826-699X
Moscow, 111123 Россия

A. E. Lopatukhin

Central Research Institute of Epidemiology

Email: fake@neicon.ru
ORCID iD: 0000-0002-7912-4270
Moscow, 111123 Россия

M. R. Bobkova

National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya

Author for correspondence.
Email: mrbobkova@mail.ru
ORCID iD: 0000-0001-5481-8957

MD, PhD, Dr Biol Sci, chirf researcher, head of T-lymphotropoc viruses
laboratory, Ivanovsky Institute of Virology

Moscow, 123098, 18, Gamaleya street, Russia

Россия

References

  1. Saksena N.K., Ge Y.C., Wang B., Xiang S.H., Dwyer D.E., Randle C., et al. An HIV-1 infected long-term non-progressor (LTNP): molecular analysis of HIV-1 strains in the vpr and nef genes. Ann. Acad. Med. Singapore. 1996; 25(6): 848-54.
  2. Wang B. Viral factors in non-progression. Front. Immunol. 2013; 4: 355. Doi: https://doi.org/10.3389/fimmu.2013.00355
  3. Arhel N.J., Kirchhoff F. Implications of Nef: host cell interactions in viral persistence and progression to AIDS. Curr. Top. Microbiol. Immunol. 2009; 339: 147-75. Doi: https://doi.org/10.1007/978-3-642-02175-6_8
  4. Basmaciogullari S., Pizzato M. The activity of Nef on HIV-1 infectivity. Front. Microbiol. 2014; 5: 232. Doi: https://doi.org/10.3389/fmicb.2014.00232
  5. Pereira E.A., daSilva L.L. HIV-1 Nef: Taking Control of Protein Trafficking. Traffic. 2016; 17(9): 976-96. Doi: https://doi.org/10.1111/tra.12412
  6. Jager S., Cimermancic P., Gulbahce N., Johnson J.R., McGovern K.E., Clarke S.C., et al. Global landscape of HIV-human protein complexes. Nature. 2011; 481(7381): 365-70. Doi: https://doi.org/10.1038/nature10719
  7. Dekaban G.A., Dikeakos J.D. HIV-I Nef inhibitors: a novel class of HIV-specific immune adjuvants in support of a cure. AIDS Res. Ther. 2017; 14(1): 53. Doi: https://doi.org/10.1186/s12981-017-0175-6
  8. Van den Broeke C., Radu M., Chernoff J., Favoreel H.W. An emerging role for p21-activated kinases (Paks) in viral infections. Trends Cell Biol. 2010; 20(3): 160-9. Doi: https://doi.org/10.1016/j.tcb.2009.12.005
  9. Stolp B., Fackler O.T. How HIV takes advantage of the cytoskeleton in entry and replication. Viruses. 2011; 3(4): 293-311. Doi: https://doi.org/10.3390/v3040293
  10. Sourisseau M., Sol-Foulon N., Porrot F., Blanchet F., Schwartz O. Inefficient human immunodeficiency virus replication in mobile lymphocytes. J. Virol. 2007; 81(2):1000-12. Doi: https://doi.org/10.1128/JVI.01629-06
  11. Vermeire J., Vanbillemont G., Witkowski W.,Verhasselt B. The Nefinfectivity enigma: mechanisms of enhanced lentiviral infection. Curr. HIV Res. 2011; 9(7): 474-89. Doi: https://doi.org/10.2174/157016211798842099
  12. Rosa A., Chande A., Ziglio S., De Sanctis V., Bertorelli R., Goh S.L., et al. HIV-1 Nef promotes infection by excluding SERINC5 from virion incorporation. Nature. 2015; 526(7572): 212-7. Doi: https://doi.org/10.1038/nature15399
  13. Lama J. The physiological relevance of CD4 receptor down-modulation during HIV infection. Curr. HIV Res. 2003; 1(2): 167-84. Doi: https://doi.org/10.2174/1570162033485276
  14. Toyoda M., Ogata Y., Mahiti M., Maeda Y., Kuang X.T., Miura T., et al. Differential Ability of Primary HIV-1 Nef Isolates To Downregulate HIV-1 Entry Receptors. J. Virol. 2015; 89(18): 9639-52. Doi: https://doi.org/10.1128/JVI.01548-15
  15. Dikeakos J.D., Thomas L., Kwon G., Elferich J., Shinde U., Thomas G. An interdomain binding site on HIV-1 Nef interacts with PACS-1 and PACS-2 on endosomes to down-regulate MHC-I. Mol. Biol. Cell. 2012; 23(11): 2184-97. Doi: https://doi.org/10.1091/mbc.E11-11-0928
  16. Lewis M.J., Lee P., Ng H.L.,Yang O.O. Immune selection in vitro reveals human immunodeficiency virus type 1 Nef sequence motifs important for its immune evasion function in vivo. J. Virol. 2012; 86(13): 7126-35. Doi: https://doi.org/10.1128/JVI.00878-12
  17. Olivetta E., Arenaccio C., Manfredi F., Anticoli S., Federico M. The Contribution of Extracellular Nef to HIV-Induced Pathogenesis. Curr. Drug Targets. 2016; 17(1): 46-53. Doi: https://doi.org/10.2174/1389450116666151001110126
  18. Lamers S.L., Poon A.F., McGrath M.S. HIV-1 nef protein structures associated with brain infection and dementia pathogenesis. PLoS One. 2011; 6(2): e16659. Doi: https://doi.org/10.1371/journal.pone.0016659
  19. Anand A.R., Rachel G., Parthasarathy D. HIV Proteins and Endothelial Dysfunction: Implications in Cardiovascular Disease. Front. Cardiovasc. Med. 2018; 5: 185. Doi: https://doi.org/10.3389/fcvm.2018.00185
  20. Almodovar S., Knight R., Allshouse A.A., Roemer S., Lozupone C., McDonald D., et al. Human Immunodeficiency Virus nef signature sequences are associated with pulmonary hypertension. AIDS Res. Hum. Retroviruses. 2012; 28(6): 607-18. Doi: https://doi.org/10.1089/AID.2011.0021
  21. Emert-Sedlak L.A., Loughran H.M., Shi H., Kulp J.L., Shu S.T., Zhao J., et al. Synthesis and evaluation of orally active small molecule HIV-1 Nef antagonists. Bioorg. Med. Chem. Lett. 2016; 26(5): 1480-4. Doi: https://doi.org/10.1016/j.bmcl.2016.01.043
  22. Hunegnaw R., Vassylyeva M., Dubrovsky L., Pushkarsky T., Sviridov D., Anashkina A.A., et al. Interaction Between HIV-1 Nef and Calnexin: From Modeling to Small Molecule Inhibitors Reversing HIV-Induced Lipid Accumulation. Arterioscler. Thromb. Vasc. Biol. 2016; 36(9): 1758-71. Doi: https://doi.org/10.1161/ATVBAHA.116.307997
  23. Corro G., Rocco C.A., De Candia C., Catano G., Turk G., Mangano A., et al. Genetic and functional analysis of HIV type 1 nef gene derived from long-term nonprogressor children: association of attenuated variants with slow progression to pediatric AIDS. AIDS Res. Hum. Retroviruses. 2012; 28(12): 1617-26. Doi: https://doi.org/10.1089/AID.2012.0020
  24. Foster J.L., Denial S.J., Temple B.R., Garcia J.V. Mechanisms of HIV-1 Nef function and intracellular signaling. J. Neuroimmune Pharmacol. 2011; 6(2): 230-46. Doi: https://doi.org/10.1007/s11481-011-9262-y
  25. O’Neill E., Kuo L.S., Krisko J.F., Tomchick D.R., Garcia J.V., Foster J.L. Dynamic evolution of the human immunodeficiency virus type 1 pathogenic factor, Nef. J. Virol. 2006; 80(3): 1311-20. Doi: https://doi.org/10.1128/JVI.80.3.1311-1320.2006
  26. Usmani S.M., Murooka T.T., Deruaz M., Koh W.H., Sharaf R.R., Di Pilato M., et al. HIV-1 Balances the Fitness Costs and Benefits of Disrupting the Host Cell Actin Cytoskeleton Early after Mucosal Transmission. Cell. Host Microbe. 2019; 25(1): 73-86. Doi: https://doi.org/10.1016/j.chom.2018.12.008
  27. Kumar S., Stecher G.,Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol. Biol. Evol. 2016; 33(7): 1870-4. Doi: https://doi.org/10.1093/molbev/msw054
  28. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Mol. Biol. Evol. 2013; 30(12): 2725-9. Doi: https://doi.org/10.1093/molbev/mst197
  29. Golosova O., Henderson R., Vaskin Y., Gabrielian A., Grekhov G., Nagarajan V., et al. Unipro UGENE NGS pipelines and components for variant calling, RNA-seq and ChIP-seq data analyses. PeerJ. 2014; 2: e644. Doi: https://doi.org/10.7717/peerj.644
  30. Nguyen L.T., Schmidt H.A., von Haeseler A., Minh B.Q. IQTREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies. Mol. Biol. Evol. 2015; 32(1): 268-74. Doi: https://doi.org/10.1093/molbev/msu300
  31. Ratner L., Haseltine W., Patarca R., Livak K.J., Starcich B., Josephs S.F., et al. Complete Nucleotide-Sequence of the AIDS Virus, HTLV-III. Nature. 1985; 313(6000): 277-84. Doi: https://doi.org/10.1038/313277a0

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Copyright (c) 2019 Gromov K.B., Kazennova E.V., Kireev D.E., Murzakova A.V., Lopatukhin A.E., Bobkova M.R.

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