Role of APOBEC3 in genetic diversity among endogenous murine leukemia viruses

PLoS Genetics

Volumn 3, Issue 10, 2007, Pages 2014-2022

  Jern, Patric ^a   Stoye, Jonathan P ^b   Coffin, John M ^a  

^a TUFTS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b NATIONAL INSTITUTE FOR MEDICAL RESEARCH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CYTIDINE DEAMINASE; PROTEIN APOBEC3; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; GENE SEQUENCE; GENETIC VARIABILITY; MOLECULAR PHYLOGENY; MURINE LEUKEMIA VIRUS; MUTATIONAL ANALYSIS; NONHUMAN; NONSENSE MUTATION; NUCLEOTIDE SEQUENCE; RETROVIRUS; VIRAL GENETICS; VIRUS IDENTIFICATION; VIRUS INACTIVATION; VIRUS INFECTIVITY; VIRUS REPLICATION;

ADENINE; ANIMALS; BINDING SITES; CYTIDINE DEAMINASE; GENOME; GUANINE; LEUKEMIA VIRUS, MURINE; MICE; MICE, INBRED C57BL; MUTATION; PHYLOGENY; PROVIRUSES; VARIATION (GENETICS); VIRUS REPLICATION;

MURINAE; MURINE LEUKEMIA VIRUS;

EID: 35948967657     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.0030183     Document Type: Article

References (50)

1. Boeke JD, Stoye JP (1997) Retrotransposons, endogenous retroviruses, and the evolution of retroelements. In: Coffin JM, Hughes SH, Varmus HE, editors. Retroviruses. New York: Cold Spring Harbor Laboratory Press. pp. 343-436.
2. CSAC (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69-87.
3. International Chicken Genome Sequencing Consortium (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432: 695-716.
4. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921.
5. Telesnitsky A, Goff SP (1997) Reverse transcriptase and the generation of retroviral DNA. In: Coffin JM, Hughes SH, Varmus HE, editors. Retroviruses. New York: Cold Spring Harbor Laboratory Press. pp. 121-160.
6. Harris RS, Bishop KN, Sheehy AM, Craig HM, Petersen-Mahrt SK, et al. (2003) DNA deamination mediates innate immunity to retroviral infection. Cell 113: 803-809.
7. Mangeat B, Turelli P, Caron G, Friedli M, Perrin L, et al. (2003) Broad antiretroviral defence by human APOBEC3G through lethal editing of nascent reverse transcripts. Nature 424: 99-103.
8. Zhang H, Yang B, Pomerantz RJ, Zhang C, Arunachalam SC, et al. (2003) The cytidine deaminase CEM15 induces hypermutation in newly synthesized HIV-1 DNA. Nature 424: 94-98.
9. Bishop KN, Holmes RK, Sheehy AM, Davidson NO, Cho SJ, et al. (2004) Cytidine deamination of retroviral DNA by diverse APOBEC proteins. Curr Biol 14: 1392-1396.
10. Liddament MT, Brown WL, Schumacher AJ, Harris RS (2004) APOBEC3F properties and hypermutation preferences indicate activity against HIV-1 in vivo. Curr Biol 14: 1385-1391.
11. Esnault C, Heidmann O, Delebecque F, Dewannieux M, Ribet D, et al. (2005) APOBEC3G cytidine deaminase inhibits retrotransposition of endogenous retroviruses. Nature 433: 430-433.
12. Okeoma CM, Lovsin N, Peterlin BM, Ross SR (2007) APOBEC3 inhibits mouse mammary tumour virus replication in vivo. Nature 445: 927-930.
13. Sperber GO, Airola T, Jern P, Blomberg J (2007) Automated recognition of retroviral sequences in genomic data-RetroTector. Nucleic Acids Res 35: 4964-4976.
14. Stoye JP, Coffin JM (1988) Polymorphism of murine endogenous proviruses revealed by using virus class-specific oligonucleotide probes. J Virol 62: 168-175.
15. Hoggan MD, O'Neill RR, Kozak CA (1986) Nonecotropic murine leukemia viruses in BALB/c and NFS/N mice: characterization of the BALB/c Bxv-1 provirus and the single NFS endogenous xenotrope. J Virol 60: 980-986.
16. Tomonaga K, Coffin JM (1999) Structures of endogenous nonecotropic murine leukemia virus (MLV) long terminal repeats in wild mice: implication for evolution of MLVs. J Virol 73: 4327-4340.
17. Stoye JP, Coffin JM (1987) The four classes of endogenous murine leukemia virus: structural relationships and potential for recombination. J Virol 61: 2659-2669.
18. Frankel WN, Stoye JP, Taylor BA, Coffin JM (1990) A linkage map of endogenous murine leukemia proviruses. Genetics 124: 221-236.
19. Datta SK, Schwartz RS (1977) Mendelian segregation of loci controlling xenotropic virus production in NZB crosses. Virology 83: 449-452.
20. Kozak CA, Hartley JW, Morse HC 3rd (1984) Laboratory and wild-derived mice with multiple loci for production of xenotropic murine leukemia virus. J Virol 51: 77-80.
21. Hartley JW, Wolford NK, Old LJ, Rowe WP (1977) A new class of murine leukemia virus associated with development of spontaneous lymphomas. Proc Natl Acad Sci U S A 74: 789-792.
22. Evans LH, Lavignon M, Taylor M, Alamgir AS (2003) Antigenic subclasses of polytropic murine leukemia virus (MLV) isolates reflect three distinct groups of endogenous polytropic MLV-related sequences in NFS/N mice. J Virol 77: 10327-10338.
23. Alamgir AS, Owens N, Lavignon M, Malik F, Evans LH (2005) Precise identification of endogenous proviruses of NFS/N mice participating in recombination with moloney ecotropic murine leukemia virus (MuLV) to generate polytropic MuLVs. J Virol 79: 4664-4671.
24. Jern P, Sperber GO, Ahlsen G, Blomberg J (2005) Sequence variability, gene structure, and expression of full-length human endogenous retrovirus H. J Virol 79: 6325-6337.
25. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876-4882.
26. Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13: 555-556.
27. Belshaw R, Katzourakis A (2005) BlastAlign: a program that uses blast to align problematic nucleotide sequences. Bioinformatics 21: 122-123.
28. Kumar S, Tamura K, Nei M (2004) MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5: 150-163.
29. Guindon S, Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704.
30. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
31. Yang Z (1998) Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol Biol Evol 15: 568-573.
32. Yu Q, Konig R, Pillai S, Chiles K, Kearney M, et al. (2004) Single-strand specificity of APOBEC3G accounts for minus-strand deamination of the HIV genome. Nat Struct Mol Biol 11: 435-442.
33. Suspene R, Rusniok C, Vartanian JP, Wain-Hobson S (2006) Twin gradients in APOBEC3 edited HIV-1 DNA reflect the dynamics of lentiviral replication. Nucleic Acids Res 34: 4677-4684.
34. Chelico L, Pham P, Calabrese P, Goodman MF (2006) APOBEC3G DNA deaminase acts processively 3′ -> 5′ on single-stranded DNA. Nat Struct Mol Biol 13: 392-399.
35. Belshaw R, Pereira V, Katzourakis A, Talbot G, Paces J, et al. (2004) Longterm reinfection of the human genome by endogenous retroviruses. Proc Natl Acad Sci U S A 101: 4894-4899.
36. Panet A, Berliner H (1978) Binding of tRNA to reverse transcriptase of RNA tumor viruses. J Virol 26: 214-220.
37. Colicelli J, Goff SP (1986) Isolation of a recombinant murine leukemia virus utilizing a new primer tRNA. J Virol 57: 37-45.
38. Bishop KN, Holmes RK, Sheehy AM, Malim MH (2004) APOBEC-mediated editing of viral RNA. Science 305: 645.
39. Jonsson SR, Hache G, Stenglein MD, Fahrenkrug SC, Andresdottir V, et al. (2006) Evolutionarily conserved and non-conserved retrovirus restriction activities of artiodactyl APOBEC3F proteins. Nucleic Acids Res 34: 5683-5694.
40. Frankel WN, Coffin JM (1994) Endogenous nonecotropic proviruses mapped with oligonucleotide probes from the long terminal repeat region. Mamm Genome 5: 275-281.
41. Frankel WN, Stoye JP, Taylor BA, Coffin JM (1989) Genetic analysis of endogenous xenotropic murine leukemia viruses: association with two common mouse mutations and the viral restriction locus Fv-1. J Virol 63: 1763-1774.
42. Stoye JP, Kaushik N, Jeremiah S, Best S (1995) Genetic map of the region surrounding the retrovirus restriction locus, Fv1, on mouse chromosome 4. Mamm Genome 6: 31-36.
43. Mariani R, Chen D, Schrofelbauer B, Navarro F, Konig R, et al. (2003) Species-specific exclusion of APOBEC3G from HIV-1 virions by Vif. Cell 114: 21-31.
44. Holmes RK, Malim MH, Bishop KN (2007) APOBEC-mediated viral restriction: not simply editing? Trends Biochem Sci 32: 118-128.
45. Harris RS, Petersen-Mahrt SK, Neuberger MS (2002) RNA editing enzyme APOBEC1 and some of its homologs can act as DNA mutators. Mol Cell 10: 1247-1253.
46. Esnault C, Millet J, Schwartz O, Heidmann T (2006) Dual inhibitory effects of APOBEC family proteins on retrotransposition of mammalian endogenous retroviruses. Nucleic Acids Res 34: 1522-1531.
47. Derse D, Hill SA, Princler G, Lloyd P, Heidecker G (2007) Resistance of human T cell leukemia virus type 1 to APOBEC3G restriction is mediated by elements in nucleocapsid. Proc Natl Acad Sci U S A 104: 2915-2920.
48. Doehle BP, Schafer A, Wiegand HL, Bogerd HP, Cullen BR (2005) Differential sensitivity of murine leukemia virus to APOBEC3-mediated inhibition is governed by virion exclusion. J Virol 79: 8201-8207.
49. Kobayashi M, Takaori-Kondo A, Shindo K, Abudu A, Fukunaga K, et al. (2004) APOBEC3G targets specific virus species. J Virol 78: 8238-8244.
50. Dong B, Kim S, Hong S, Das Gupta J, Malathi K, et al. (2007) An infectious retrovirus susceptible to an IFN antiviral pathway from human prostate tumors. Proc Natl Acad Sci U S A 104: 1655-1660.