Novel Mutant Human Immunodeficiency Virus Type 1 Strains with High Degree of Resistance to Cynomolgus Macaque TRIMCyp Generated by Random Mutagenesis

Overview

Journal J Gen Virol

Specialty Microbiology

Date 2016 Jan 23

PMID 26795727

Citations 8

Authors

Tahmina Sultana

Emi E Nakayama

Satoshi Tobita

Masaru Yokoyama

Yohei Seki

Akatsuki Saito

Masako Nomaguchi

Akio Adachi

Hirofumi Akari

Hironori Sato

Tatsuo Shioda

Affiliations

Soon will be listed here.

Abstract

Old World monkey TRIM5α strongly suppresses human immunodeficiency virus type 1 (HIV-1) replication. A fusion protein comprising cynomolgus macaque (CM) TRIM5 and cyclophilin A (CM TRIMCyp) also potently suppresses HIV-1 replication. However, CM TRIMCyp fails to suppress a mutant HIV-1 that encodes a mutant capsid protein containing a SIVmac239-derived loop between α-helices 4 and 5 (L4/5). There are seven amino acid differences between L4/5 of HIV-1 and SIVmac239. Here, we investigated the minimum numbers of amino acid substitutions that would allow HIV-1 to evade CM TRIMCyp-mediated suppression. We performed random PCR mutagenesis to construct a library of HIV-1 variants containing mutations in L4/5, and then we recovered replication-competent viruses from CD4+ MT4 cells that expressed high levels of CM TRIMCyp. CM TRIMCyp-resistant viruses were obtained after three rounds of selection in MT4 cells expressing CM TRIMCyp and these were found to contain four amino acid substitutions (H87R, A88G, P90D and P93A) in L4/5. We then confirmed that these substitutions were sufficient to confer CM TRIMCyp resistance to HIV-1. In a separate experiment using a similar method, we obtained novel CM TRIM5α-resistant HIV-1 strains after six rounds of selection and rescue. Analysis of these mutants revealed that V86A and G116E mutations in the capsid region conferred partial resistance to CM TRIM5α without substantial fitness cost when propagated in MT4 cells expressing CM TRIM5α. These results confirmed and further extended the previous notion that CM TRIMCyp and CM TRIM5α recognize the HIV-1 capsid in different manners.

Citing Articles

Host ZCCHC3 blocks HIV-1 infection and production through a dual mechanism.

Yi B, Tanaka Y, Cornish D, Kosako H, Butlertanaka E, Sengupta P iScience. 2024; 27(3):109107.

PMID: 38384847 PMC: 10879702. DOI: 10.1016/j.isci.2024.109107.

HIV-1 capsid variability: viral exploitation and evasion of capsid-binding molecules.

Saito A, Yamashita M Retrovirology. 2021; 18(1):32.

PMID: 34702294 PMC: 8549334. DOI: 10.1186/s12977-021-00577-x.

Changes in dynamic and static structures of the HIV-1 p24 capsid protein N-domain caused by amino-acid substitution are associated with its viral viability.

Sato Y, Matsugami A, Watanabe S, Hayashi F, Arai M, Kigawa T Protein Sci. 2021; 30(11):2233-2245.

PMID: 34523753 PMC: 8522491. DOI: 10.1002/pro.4184.

The 4th and 112th Residues of Viral Capsid Cooperatively Modulate Capsid-CPSF6 Interactions of HIV-1.

Saito A, Sultana T, Ode H, Nohata K, Samune Y, Nakayama E AIDS Res Hum Retroviruses. 2020; 36(6):513-521.

PMID: 31941344 PMC: 7262650. DOI: 10.1089/AID.2019.0250.

Multiple Pathways To Avoid Beta Interferon Sensitivity of HIV-1 by Mutations in Capsid.

Sultana T, Mamede J, Saito A, Ode H, Nohata K, Cohen R J Virol. 2019; 93(23).

PMID: 31511380 PMC: 6854511. DOI: 10.1128/JVI.00986-19.

References

Neil S, Zang T, Bieniasz P . Tetherin inhibits retrovirus release and is antagonized by HIV-1 Vpu. Nature. 2008; 451(7177):425-30. DOI: 10.1038/nature06553. View

Stremlau M, Owens C, Perron M, Kiessling M, Autissier P, Sodroski J . The cytoplasmic body component TRIM5alpha restricts HIV-1 infection in Old World monkeys. Nature. 2004; 427(6977):848-53. DOI: 10.1038/nature02343. View

Van Damme N, Guatelli J . HIV-1 Vpu inhibits accumulation of the envelope glycoprotein within clathrin-coated, Gag-containing endosomes. Cell Microbiol. 2007; 10(5):1040-57. DOI: 10.1111/j.1462-5822.2007.01101.x. View

Qi M, Yang R, Aiken C . Cyclophilin A-dependent restriction of human immunodeficiency virus type 1 capsid mutants for infection of nondividing cells. J Virol. 2008; 82(24):12001-8. PMC: 2593355. DOI: 10.1128/JVI.01518-08. View

Kuroishi A, Saito A, Shingai Y, Shioda T, Nomaguchi M, Adachi A . Modification of a loop sequence between alpha-helices 6 and 7 of virus capsid (CA) protein in a human immunodeficiency virus type 1 (HIV-1) derivative that has simian immunodeficiency virus (SIVmac239) vif and CA alpha-helices 4 and 5 loop improves.... Retrovirology. 2009; 6:70. PMC: 2731049. DOI: 10.1186/1742-4690-6-70. View

Price A, Marzetta F, Lammers M, Ylinen L, Schaller T, Wilson S . Active site remodeling switches HIV specificity of antiretroviral TRIMCyp. Nat Struct Mol Biol. 2009; 16(10):1036-42. PMC: 3556581. DOI: 10.1038/nsmb.1667. View

Li Y, Kar A, Sodroski J . Target cell type-dependent modulation of human immunodeficiency virus type 1 capsid disassembly by cyclophilin A. J Virol. 2009; 83(21):10951-62. PMC: 2772774. DOI: 10.1128/JVI.00682-09. View

Nakayama E, Shioda T . Anti-retroviral activity of TRIM5 alpha. Rev Med Virol. 2010; 20(2):77-92. DOI: 10.1002/rmv.637. View

Kuroishi A, Bozek K, Shioda T, Nakayama E . A single amino acid substitution of the human immunodeficiency virus type 1 capsid protein affects viral sensitivity to TRIM5 alpha. Retrovirology. 2010; 7:58. PMC: 2910007. DOI: 10.1186/1742-4690-7-58. View

10.

Kirmaier A, Wu F, Newman R, Hall L, Morgan J, OConnor S . TRIM5 suppresses cross-species transmission of a primate immunodeficiency virus and selects for emergence of resistant variants in the new species. PLoS Biol. 2010; 8(8). PMC: 2927514. DOI: 10.1371/journal.pbio.1000462. View

11.

Kono K, Song H, Yokoyama M, Sato H, Shioda T, Nakayama E . Multiple sites in the N-terminal half of simian immunodeficiency virus capsid protein contribute to evasion from rhesus monkey TRIM5α-mediated restriction. Retrovirology. 2010; 7:72. PMC: 2944288. DOI: 10.1186/1742-4690-7-72. View

12.

Pacheco B, Finzi A, Stremlau M, Sodroski J . Adaptation of HIV-1 to cells expressing rhesus monkey TRIM5α. Virology. 2010; 408(2):204-12. PMC: 2975777. DOI: 10.1016/j.virol.2010.09.019. View

13.

Miyamoto T, Yokoyama M, Kono K, Shioda T, Sato H, Nakayama E . A single amino acid of human immunodeficiency virus type 2 capsid protein affects conformation of two external loops and viral sensitivity to TRIM5α. PLoS One. 2011; 6(7):e22779. PMC: 3145752. DOI: 10.1371/journal.pone.0022779. View

14.

Schaller T, Ocwieja K, Rasaiyaah J, Price A, Brady T, Roth S . HIV-1 capsid-cyclophilin interactions determine nuclear import pathway, integration targeting and replication efficiency. PLoS Pathog. 2011; 7(12):e1002439. PMC: 3234246. DOI: 10.1371/journal.ppat.1002439. View

15.

Saito A, Kono K, Nomaguchi M, Yasutomi Y, Adachi A, Shioda T . Geographical, genetic and functional diversity of antiretroviral host factor TRIMCyp in cynomolgus macaque (Macaca fascicularis). J Gen Virol. 2011; 93(Pt 3):594-602. PMC: 3352356. DOI: 10.1099/vir.0.038075-0. View

16.

Nomaguchi M, Yokoyama M, Kono K, Nakayama E, Shioda T, Saito A . Gag-CA Q110D mutation elicits TRIM5-independent enhancement of HIV-1mt replication in macaque cells. Microbes Infect. 2012; 15(1):56-65. DOI: 10.1016/j.micinf.2012.10.013. View

17.

Veillette M, Bichel K, Pawlica P, Freund S, Plourde M, Pham Q . The V86M mutation in HIV-1 capsid confers resistance to TRIM5α by abrogation of cyclophilin A-dependent restriction and enhancement of viral nuclear import. Retrovirology. 2013; 10:25. PMC: 3598646. DOI: 10.1186/1742-4690-10-25. View

18.

Saito A, Nomaguchi M, Kono K, Iwatani Y, Yokoyama M, Yasutomi Y . TRIM5 genotypes in cynomolgus monkeys primarily influence inter-individual diversity in susceptibility to monkey-tropic human immunodeficiency virus type 1. J Gen Virol. 2013; 94(Pt 6):1318-1324. DOI: 10.1099/vir.0.050252-0. View

19.

Soll S, Wilson S, Kutluay S, Hatziioannou T, Bieniasz P . Assisted evolution enables HIV-1 to overcome a high TRIM5α-imposed genetic barrier to rhesus macaque tropism. PLoS Pathog. 2013; 9(9):e1003667. PMC: 3784476. DOI: 10.1371/journal.ppat.1003667. View

20.

Nomaguchi M, Yokoyama M, Kono K, Nakayama E, Shioda T, Doi N . Generation of rhesus macaque-tropic HIV-1 clones that are resistant to major anti-HIV-1 restriction factors. J Virol. 2013; 87(21):11447-61. PMC: 3807366. DOI: 10.1128/JVI.01549-13. View