Comprehensive Investigation on the Interplay between Feline APOBEC3Z3 Proteins and Feline Immunodeficiency Virus Vif Proteins

Most of the emergences of new virus infections originate from the cross-species transmission of viruses. The fact that some virus infections are strictly specific for the host species indicates that certain “species barriers” in the hosts restrict cross-species jump of viruses, while viruses have evolutionary acquired their own “arms” to overcome/antagonize/neutralize these hurdles. ABSTRACT As the hosts of lentiviruses, almost 40 species of felids (family Felidae) are distributed around the world, and more than 20 feline species test positive for feline immunodeficiency virus (FIV), a lineage of lentiviruses. These observations suggest that FIVs globally infected a variety of feline species through multiple cross-species transmission events during a million-year history. Cellular restriction factors potentially inhibit lentiviral replication and limit cross-species lentiviral transmission, and cellular APOBEC3 deaminases are known as a potent restriction factor. In contrast, lentiviruses have evolutionary-acquired viral infectivity factor (Vif) to neutralize the APOBEC3-mediated antiviral effect. Because the APOBEC3-Vif interaction is strictly specific for viruses and their hosts, a comprehensive investigation focusing on Vif-APOBEC3 interplay can provide clues that will elucidate the roles of this virus-host interplay on cross-species transmission of lentiviruses. Here, we performed a comprehensive investigation with 144 patterns of a round robin test using 18 feline APOBEC3Z3 genes, an antiviral APOBEC3 gene in felid, and 8 FIV Vifs and derived a matrix showing the interplay between feline APOBEC3Z3 and FIV Vif. We particularly focused on the interplay between the APOBEC3Z3 of three felids (domestic cat, ocelot, and Asian golden cat) and an FIV Vif (strain Petaluma), and revealed that residues 65 and 66 of the APOBEC3Z3 protein of multiple felids are responsible for the counteraction triggered by FIV Petaluma Vif. Altogether, our findings can be a clue to elucidate not only the scenarios of the cross-species transmissions of FIVs in felids but also the evolutionary interaction between mammals and lentiviruses. IMPORTANCE Most of the emergences of new virus infections originate from the cross-species transmission of viruses. The fact that some virus infections are strictly specific for the host species indicates that certain “species barriers” in the hosts restrict cross-species jump of viruses, while viruses have evolutionary acquired their own “arms” to overcome/antagonize/neutralize these hurdles. Therefore, understanding of the molecular mechanism leading to successful cross-species viral transmission is crucial for considering the menus of the emergence of novel pathogenic viruses. In the field of retrovirology, APOBEC3-Vif interaction is a well-studied example of the battles between hosts and viruses. Here, we determined the sequences of 11 novel feline APOBEC3Z3 genes and demonstrated that all 18 different feline APOBEC3Z3 proteins tested exhibit anti-feline immunodeficiency virus (FIV) activity. Our comprehensive investigation focusing on the interplay between feline APOBEC3 and FIV Vif can be a clue to elucidate the scenarios of the cross-species transmissions of FIVs in felids.

[1]  M. Fukushi,et al.  SARS-CoV-2 ORF3b Is a Potent Interferon Antagonist Whose Activity Is Increased by a Naturally Occurring Elongation Variant , 2020, Cell Reports.

[2]  Y. Koyanagi,et al.  A role for gorilla APOBEC3G in shaping lentivirus evolution including transmission to humans , 2020, PLoS pathogens.

[3]  Xianghui Yu,et al.  The C-terminal domain of feline and bovine SAMHD1 proteins has a crucial role in lentiviral restriction , 2020, The Journal of Biological Chemistry.

[4]  M. Emerman,et al.  Retrocopying expands the functional repertoire of APOBEC3 antiviral proteins in primates , 2020, bioRxiv.

[5]  Kei Sato,et al.  Retroviruses drive the rapid evolution of mammalian APOBEC3 genes , 2019, Proceedings of the National Academy of Sciences.

[6]  F. Kirchhoff,et al.  Key Viral Adaptations Preceding the AIDS Pandemic. , 2019, Cell host & microbe.

[7]  R. Schinazi,et al.  Interplay of ancestral non-primate lentiviruses with the virus-restricting SAMHD1 proteins of their hosts , 2018, The Journal of Biological Chemistry.

[8]  Y. Koyanagi,et al.  A naturally occurring feline APOBEC3 variant that loses anti-lentiviral activity by lacking two amino acid residues. , 2018, The Journal of general virology.

[9]  Y. Koyanagi,et al.  New World feline APOBEC3 potently controls inter-genus lentiviral transmission , 2018, Retrovirology.

[10]  F. Kirchhoff,et al.  Human-Specific Adaptations in Vpu Conferring Anti-tetherin Activity Are Critical for Efficient Early HIV-1 Replication In Vivo. , 2018, Cell host & microbe.

[11]  T. Marquès-Bonet,et al.  Stably expressed APOBEC3H forms a barrier for cross-species transmission of simian immunodeficiency virus of chimpanzee to humans , 2017, PLoS pathogens.

[12]  Yusuke Nakano,et al.  A conflict of interest: the evolutionary arms race between mammalian APOBEC3 and lentiviral Vif , 2017, Retrovirology.

[13]  S. Iwami,et al.  HIV-1 competition experiments in humanized mice show that APOBEC3H imposes selective pressure and promotes virus adaptation , 2017, PLoS pathogens.

[14]  W. Boyce,et al.  Feline Immunodeficiency Virus Cross-Species Transmission: Implications for Emergence of New Lentiviral Infections , 2016, Journal of Virology.

[15]  Y. Koyanagi,et al.  A naturally occurring bovine APOBEC3 confers resistance to bovine lentiviruses: implication for the co-evolution of bovids and their lentiviruses , 2016, Scientific Reports.

[16]  M. Carpenter,et al.  The DNA cytosine deaminase APOBEC3H haplotype I likely contributes to breast and lung cancer mutagenesis , 2016, Nature Communications.

[17]  Y. Koyanagi,et al.  Small ruminant lentiviral Vif proteins commonly utilize cyclophilin A, an evolutionarily and structurally conserved protein, to degrade ovine and caprine APOBEC3 proteins , 2016, Microbiology and immunology.

[18]  Sudhir Kumar,et al.  MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. , 2016, Molecular biology and evolution.

[19]  Hiroshi Tanaka,et al.  Coevolutionary dynamics between tribe Cercopithecini tetherins and their lentiviruses , 2015, Scientific Reports.

[20]  M. Carpenter,et al.  A Naturally Occurring Domestic Cat APOBEC3 Variant Confers Resistance to Feline Immunodeficiency Virus Infection , 2015, Journal of Virology.

[21]  Y. Iwasa,et al.  Pandemic HIV-1 Vpu overcomes intrinsic herd immunity mediated by tetherin , 2015, Scientific Reports.

[22]  Hiroshi Tanaka,et al.  Vif determines the requirement for CBF-β in APOBEC3 degradation. , 2015, The Journal of general virology.

[23]  M. Emerman,et al.  Natural Polymorphisms in Human APOBEC3H and HIV-1 Vif Combine in Primary T Lymphocytes to Affect Viral G-to-A Mutation Levels and Infectivity , 2014, PLoS genetics.

[24]  D. M. Junqueira,et al.  Analysis of single-nucleotide polymorphisms in the APOBEC3H gene of domestic cats (Felis catus) and their association with the susceptibility to feline immunodeficiency virus and feline leukemia virus infections. , 2014, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[25]  Hiroshi Tanaka,et al.  Characterization of red-capped mangabey tetherin: implication for the co-evolution of primates and their lentiviruses , 2014, Scientific Reports.

[26]  C. Boesch,et al.  The ecology of primate retroviruses - an assessment of 12 years of retroviral studies in the Taï national park area, Côte d׳Ivoire. , 2014, Virology.

[27]  J. Pecon-Slattery,et al.  Evolution of Puma Lentivirus in Bobcats (Lynx rufus) and Mountain Lions (Puma concolor) in North America , 2014, Journal of Virology.

[28]  F. Hecht,et al.  HIV-1 Vif adaptation to human APOBEC3H haplotypes. , 2013, Cell host & microbe.

[29]  Reuben S Harris,et al.  The APOBEC3 family of retroelement restriction factors. , 2013, Current topics in microbiology and immunology.

[30]  Sergei L. Kosakovsky Pond,et al.  Detecting Individual Sites Subject to Episodic Diversifying Selection , 2012, PLoS genetics.

[31]  C. Münk,et al.  An ancient history of gene duplications, fusions and losses in the evolution of APOBEC3 mutators in mammals , 2012, BMC Evolutionary Biology.

[32]  M. Peeters,et al.  Cross-species transmission of simian retroviruses: how and why they could lead to the emergence of new diseases in the human population , 2012, AIDS.

[33]  M. Hosie,et al.  Feline Immunodeficiency Virus in South America , 2012, Viruses.

[34]  M. Emerman,et al.  The host restriction factor APOBEC3G and retroviral Vif protein coevolve due to ongoing genetic conflict. , 2012, Cell host & microbe.

[35]  V. Simon,et al.  The Activity Spectrum of Vif from Multiple HIV-1 Subtypes against APOBEC3G, APOBEC3F, and APOBEC3H , 2011, Journal of Virology.

[36]  Isabelle Dietrich,et al.  Feline Tetherin Efficiently Restricts Release of Feline Immunodeficiency Virus but Not Spreading of Infection , 2011, Journal of Virology.

[37]  Y. Morikawa,et al.  Cloning and Characterization of the Antiviral Activity of Feline Tetherin/BST-2 , 2011, PloS one.

[38]  Xiaojun Wang,et al.  Analysis of Human APOBEC3H Haplotypes and Anti-Human Immunodeficiency Virus Type 1 Activity , 2011, Journal of Virology.

[39]  C. Boesch,et al.  No evidence for transmission of SIVwrc from western red colobus monkeys (piliocolobus badius badius) to wild west african chimpanzees (pan troglodytes verus) despite high exposure through hunting , 2011, BMC Microbiology.

[40]  N. Yuhki,et al.  Vif of Feline Immunodeficiency Virus from Domestic Cats Protects against APOBEC3 Restriction Factors from Many Felids , 2010, Journal of Virology.

[41]  O. Gascuel,et al.  New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. , 2010, Systematic biology.

[42]  S. O’Brien,et al.  Feline immunodeficiency virus (FIV) in wild Pallas' cats. , 2010, Veterinary immunology and immunopathology.

[43]  John S. Albin,et al.  Interactions of host APOBEC3 restriction factors with HIV-1 in vivo: implications for therapeutics , 2010, Expert Reviews in Molecular Medicine.

[44]  M. Emerman,et al.  The Range of Human APOBEC3H Sensitivity to Lentiviral Vif Proteins , 2009, Journal of Virology.

[45]  M. Emerman,et al.  Antiretroelement activity of APOBEC3H was lost twice in recent human evolution. , 2008, Cell host & microbe.

[46]  Michael Emerman,et al.  HIV-1 accessory proteins--ensuring viral survival in a hostile environment. , 2008, Cell host & microbe.

[47]  S. O’Brien,et al.  Functions, structure, and read-through alternative splicing of feline APOBEC3 genes , 2008, Genome Biology.

[48]  W. Boyce,et al.  Frequent Transmission of Immunodeficiency Viruses among Bobcats and Pumas , 2007, Journal of Virology.

[49]  Agostinho Antunes,et al.  The Late Miocene Radiation of Modern Felidae: A Genetic Assessment , 2006, Science.

[50]  S. O’Brien,et al.  Seroprevalence and Genomic Divergence of Circulating Strains of Feline Immunodeficiency Virus among Felidae and Hyaenidae Species , 2005, Journal of Virology.

[51]  Sergei L. Kosakovsky Pond,et al.  Not so different after all: a comparison of methods for detecting amino acid sites under selection. , 2005, Molecular biology and evolution.

[52]  M. Malim,et al.  Isolation of a human gene that inhibits HIV-1 infection and is suppressed by the viral Vif protein , 2002, Nature.

[53]  M. Charleston,et al.  Preferential host switching by primate lentiviruses can account for phylogenetic similarity with the primate phylogeny. , 2002, Systematic biology.

[54]  M. Pistello,et al.  Analysis of the genetic diversity and phylogenetic relationship of Italian isolates of feline immunodeficiency virus indicates a high prevalence and heterogeneity of subtype B. , 1997, The Journal of general virology.

[55]  S. O’Brien,et al.  Growth of lion and puma lentiviruses in domestic cat cells and comparisons with FIV. , 1997, Virology.

[56]  R. Avery,et al.  Proviral organization and sequence analysis of feline immunodeficiency virus isolated from a Pallas' cat. , 1997, Virology.

[57]  C. Packer,et al.  A lion lentivirus related to feline immunodeficiency virus: epidemiologic and phylogenetic aspects , 1994, Journal of virology.

[58]  T. Caro,et al.  Worldwide prevalence of lentivirus infection in wild feline species: epidemiologic and phylogenetic aspects , 1992, Journal of virology.

[59]  D M Irwin,et al.  Evolution of the cytochrome b gene of mammals. , 1991, Journal of molecular evolution.