1
|
Olabode AS, Mumby MJ, Wild TA, Muñoz-Baena L, Dikeakos JD, Poon AFY. Phylogenetic Reconstruction and Functional Characterization of the Ancestral Nef Protein of Primate Lentiviruses. Mol Biol Evol 2023; 40:msad164. [PMID: 37463439 PMCID: PMC10400143 DOI: 10.1093/molbev/msad164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/19/2023] [Accepted: 07/10/2023] [Indexed: 07/20/2023] Open
Abstract
Nef is an accessory protein unique to the primate HIV-1, HIV-2, and SIV lentiviruses. During infection, Nef functions by interacting with multiple host proteins within infected cells to evade the immune response and enhance virion infectivity. Notably, Nef can counter immune regulators such as CD4 and MHC-I, as well as the SERINC5 restriction factor in infected cells. In this study, we generated a posterior sample of time-scaled phylogenies relating SIV and HIV Nef sequences, followed by reconstruction of ancestral sequences at the root and internal nodes of the sampled trees up to the HIV-1 Group M ancestor. Upon expression of the ancestral primate lentivirus Nef protein within CD4+ HeLa cells, flow cytometry analysis revealed that the primate lentivirus Nef ancestor robustly downregulated cell-surface SERINC5, yet only partially downregulated CD4 from the cell surface. Further analysis revealed that the Nef-mediated CD4 downregulation ability evolved gradually, while Nef-mediated SERINC5 downregulation was recovered abruptly in the HIV-1/M ancestor. Overall, this study provides a framework to reconstruct ancestral viral proteins and enable the functional characterization of these proteins to delineate how functions could have changed throughout evolutionary history.
Collapse
Affiliation(s)
- Abayomi S Olabode
- Department of Pathology & Laboratory Medicine, Western University, London, Canada
| | - Mitchell J Mumby
- Department of Microbiology & Immunology, Western University, London, Canada
| | - Tristan A Wild
- Department of Microbiology & Immunology, Western University, London, Canada
| | - Laura Muñoz-Baena
- Department of Microbiology & Immunology, Western University, London, Canada
| | - Jimmy D Dikeakos
- Department of Microbiology & Immunology, Western University, London, Canada
| | - Art F Y Poon
- Department of Pathology & Laboratory Medicine, Western University, London, Canada
- Department of Microbiology & Immunology, Western University, London, Canada
- Department of Computer Science, Western University, London, Canada
| |
Collapse
|
2
|
Konno Y, Nagaoka S, Kimura I, Takahashi Ueda M, Kumata R, Ito J, Nakagawa S, Kobayashi T, Koyanagi Y, Sato K. A naturally occurring feline APOBEC3 variant that loses anti-lentiviral activity by lacking two amino acid residues. J Gen Virol 2018; 99:704-709. [PMID: 29611801 DOI: 10.1099/jgv.0.001046] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) is a mammalian protein that restricts lentiviral replication. Various polymorphisms of mammalian APOBEC3 genes have been observed in humans, Old World monkeys and domestic cats; however, the genetic diversity of APOBEC3 genes in other mammals remains unaddressed. Here we identify a novel haplotype of the feline APOBEC3Z3 gene, an APOBEC3 gene that restricts feline immunodeficiency virus (FIV) replication, in a Eurasian lynx (Lynx lynx). Compared to the previously identified lynx APOBEC3Z3 (haplotype I), the new sequence (haplotype II) harbours two amino acid deletions (Q16 and H17) and a nonsynonymous substitution (R68Q). Interestingly, lynx APOBEC3Z3 haplotype II does not suppress FIV infectivity, whereas haplotype I does. Mutagenesis experiments further revealed that deleting two amino acids (Q16 and H17) causes anti-FIV activity loss. This report demonstrates that a naturally occurring APOBEC3 variant loses anti-lentiviral activity through the deletion of two amino acid residues.
Collapse
Affiliation(s)
- Yoriyuki Konno
- Laboratory of Systems Virology, Department of Biosystems Science, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Shumpei Nagaoka
- Laboratory of Systems Virology, Department of Biosystems Science, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Izumi Kimura
- Laboratory of Systems Virology, Department of Biosystems Science, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | | | - Ryuichi Kumata
- Laboratory of Systems Virology, Department of Biosystems Science, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,Faculty of Science, Kyoto University, Kyoto, Japan
| | - Jumpei Ito
- Division of Human Genetics, Department of Integrated Genetics, National Institute of Genetics, Shizuoka, Japan
| | - So Nakagawa
- Micro/Nano Technology Center, Tokai University, Kanagawa, Japan.,Department of Molecular Life Science, Tokai University School of Medicine, Tokai University, Kanagawa, Japan
| | - Tomoko Kobayashi
- Department of Animal Science, Faculty of Agriculture, Tokyo University of Agriculture, Kanagawa, Japan
| | - Yoshio Koyanagi
- Laboratory of Systems Virology, Department of Biosystems Science, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Kei Sato
- CREST, Japan Science and Technology Agency, Saitama, Japan.,Laboratory of Systems Virology, Department of Biosystems Science, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,Present address: Division of Systems Virology, Department of Infectious Disease Control, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, 1088639 Tokyo, Japan
| |
Collapse
|
3
|
Yoshikawa R, Nakano Y, Yamada E, Izumi T, Misawa N, Koyanagi Y, Sato K. Species-specific differences in the ability of feline lentiviral Vif to degrade feline APOBEC3 proteins. Microbiol Immunol 2016; 60:272-9. [PMID: 26935128 PMCID: PMC5074269 DOI: 10.1111/1348-0421.12371] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 02/21/2016] [Accepted: 02/29/2016] [Indexed: 01/24/2023]
Abstract
How host-virus co-evolutionary relationships manifest is one of the most intriguing issues in virology. To address this topic, the mammal-lentivirus relationship can be considered as an interplay of cellular and viral proteins, particularly apolipoprotein B mRNA editing enzyme catalytic polypeptide-like 3 (APOBEC3) and viral infectivity factor (Vif). APOBEC3s enzymatically restrict lentivirus replication, whereas Vif antagonizes the host anti-viral action mediated by APOBEC3. In this study, the focus was on the interplay between feline APOBEC3 proteins and two feline immunodeficiency viruses in cats and pumas. To our knowledge, this study provides the first evidence of non-primate lentiviral Vif being incapable of counteracting a natural host's anti-viral activity mediated via APOBEC3 protein.
Collapse
Affiliation(s)
- Rokusuke Yoshikawa
- Laboratory of Viral PathogenesisInstitute for Virus ResearchKyoto UniversityKyoto6068507
| | - Yusuke Nakano
- Laboratory of Viral PathogenesisInstitute for Virus ResearchKyoto UniversityKyoto6068507
| | - Eri Yamada
- Laboratory of Viral PathogenesisInstitute for Virus ResearchKyoto UniversityKyoto6068507
| | - Taisuke Izumi
- Laboratory of Viral PathogenesisInstitute for Virus ResearchKyoto UniversityKyoto6068507
- CRESTJapan Science and Technology AgencySaitama3220012Japan
| | - Naoko Misawa
- Laboratory of Viral PathogenesisInstitute for Virus ResearchKyoto UniversityKyoto6068507
| | - Yoshio Koyanagi
- Laboratory of Viral PathogenesisInstitute for Virus ResearchKyoto UniversityKyoto6068507
| | - Kei Sato
- Laboratory of Viral PathogenesisInstitute for Virus ResearchKyoto UniversityKyoto6068507
- CRESTJapan Science and Technology AgencySaitama3220012Japan
| |
Collapse
|