Rev variation during persistent lentivirus infection

Viruses

Volumn 3, Issue 1, 2011, Pages 1-11

  Carpenter, Susan ^a   Chen, Wei Chen ^b   Dorman, Karin S ^a,b  

^a IOWA STATE UNIVERSITY   (United States)

^b Department of Statistics Center for Statistics and Applications in Forensic Evidence Iowa State University 2438 Osborn Dr Ames   (United States)

Author keywords

Equine infectious anemia virus; Immune evasion; Lentivirus; Overlapping reading frames; Rev; Selection

Indexed keywords

MEMBRANE PROTEIN; REV PROTEIN;

DISEASE COURSE; EQUINE INFECTIOUS ANEMIA; EQUINE INFECTIOUS ANEMIA VIRUS; EXON; GENE EXPRESSION; GENE MUTATION; GENETIC VARIABILITY; HORSE; IMMUNE EVASION; LENTIVIRUS INFECTION; NONHUMAN; NUCLEAR EXPORT SIGNAL; OPEN READING FRAME; PERSISTENT VIRUS INFECTION; PHENOTYPIC VARIATION; PROTEIN FUNCTION; REVIEW; VIRUS REPLICATION;

ANIMALS; EQUINE INFECTIOUS ANEMIA; GENE PRODUCTS, REV; GENES, ENV; GENES, REV; HIV-1; HORSES; HUMANS; IMMUNE EVASION; INFECTIOUS ANEMIA VIRUS, EQUINE; MODELS, BIOLOGICAL; T-LYMPHOCYTES, CYTOTOXIC; TRANSCRIPTION, GENETIC; VIRUS REPLICATION;

EQUINE INFECTIOUS ANEMIA VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1; LENTIVIRUS;

EID: 79952169305     PISSN: None     EISSN: 19994915     Source Type: Journal    
DOI: 10.3390/v3010001     Document Type: Review

References (30)

1. Alexandersen, S.; Carpenter, S. Characterization of variable regions in the envelope and S3 open reading frame of equine infectious anemia virus. J. Virol. 1991, 65, 4255-4262.
2. Leroux, C.; Issel, C.J.; Montelaro, R.C. Novel and dynamic evolution of equine infectious anemia virus genomic quasispecies associated with sequential disease cycles in an experimentally infected pony. J. Virol. 1997, 71, 9627-9639.
3. Belshan, M.; Harris, M.E.; Shoemaker, A.E.; Hope, T.J.; Carpenter, S. Biological characterization of Rev variation in equine infectious anemia virus. J. Virol. 1998, 72, 4421-4426.
4. Bobbitt, K.R.; Addo, M.M.; Altfeld, M.; Filzen, T.; Onafuwa, A.A.; Walker, B.D.; Collins, K.L. Rev activity determines sensitivity of HIV-1-infected primary T cells to CTL killing. Immunity 2003, 18, 289-299.
5. Addo, M.M.; Altfeld, M.; Rosenberg, E.S.; Eldridge, R.L.; Philips, M.N.; Habeeb, K.; Khatri, A.; Brander, C.; Robbins, G.K.; Mazzara, G.P.; et al. The HIV-1 regulatory proteins Tat and Rev are frequently targeted by cytotoxic T lymphocytes derived from HIV-1-infected individuals. Proc. Natl. Acad. Sci. U. S. A. 2001, 98, 1781-1786.
6. Mealey, R.H.; Zhang, B.; Leib, S.R.; Littke, M.H.; McGuire, T.C. Epitope specificity is critical for high and moderate avidity cytotoxic T lymphocytes associated with control of viral load and clinical disease in horses with equine infectious anemia virus. Virology 2003, 313, 537-552.
7. Hein, J.; Støvlbaek, J. A maximum-likelihood approach to analyzing nonoverlapping and overlapping reading frames. J. Mol. Evol. 1995, 40, 181-189.
8. Belshan, M.; Baccam, P.; Oaks, J.L.; Sponseller, B.A.; Murphy, S.C.; Cornette, J.; Carpenter, S. Genetic and biological variation in equine infectious anemia virus Rev correlates with variable stages of clinical disease in an experimentally infected pony. Virology 2001, 279, 185-200.
9. Baccam, P.; Thompson, R.J.; Li, Y.; Sparks, W.O.; Belshan, M.; Dorman, K.S.; Wannemuehler, Y.; Oaks, J.L.; Cornette, J.L.; Carpenter, S. Subpopulations of equine infectious anemia virus Rev coexist in vivo and differ in phenotype. J. Virol. 2003, 77, 12122-12131.
10. Sparks, W.O.; Dorman, K.S.; Liu, S.; Carpenter, S. Naturally arising point mutations in non-essential domains of equine infectious anemia virus Rev alter Rev-dependent nuclear-export activity. J. Gen. Virol. 2008, 89, 1043-1048.
11. Belshan, M.; Park, G.S.; Bilodeau, P.; Stoltzfus, C.M.; Carpenter, S. Binding of equine infectious anemia virus Rev to an exon splicing enhancer mediates alternative splicing and nuclear export of viral mRNAs. Mol. Cell. Biol. 2000, 20, 3550-3557.
12. Baccam, P.; Thompson, R.J.; Fedrigo, O.; Carpenter, S.; Cornette, J.L. PAQ: Partition Analysis of Quasispecies. Bioinformatics 2001, 17, 16-22.
13. Miyata, T.; Yasunaga, T. Molecular evolution of mRNA: A method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its application. J. Mol. Evol. 1980, 16, 23-36.
14. Hurst, L.D.; Pal, C. Evidence for purifying selection acting on silent sites in BRCA1. Trends Genet. 2001, 17, 62-65.
15. Holmes, E.C.; Lipman, D.J.; Zamarin, D.; Yewdell, J.W. Comment on -Large-scale sequence analysis of avian influenza isolates. Science 2006, 313, 1573.
16. Pavesi, A. Pattern of nucleotide substitution in the overlapping nonstructural genes of influenza A virus and implication for the genetic diversity of the H5N1 subtype. Gene 2007, 402, 28-34.
17. Ngandu, N.K.; Scheffler, K.; Moore, P.; Woodman, Z.; Martin, D.; Seoighe, C. Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequences. Virol. J. 2008, 5, 160.
18. Li, W.H.; Wu, C.I.; Luo, C.C. A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol. Biol. Evol. 1985, 2, 150-174.
19. Pedersen, A.M.; Jensen, J.L. A dependent-rates model and an MCMC-based methodology for the maximum-likelihood analysis of sequences with overlapping reading frames. Mol. Biol. Evol. 2001, 18, 763-776.
20. Muse, S.V.; Gaut, B.S. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol. Biol. Evol. 1994, 11, 715-724.
21. Nielsen, R.; Yang, Z. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 1998, 148, 929-936.
22. Sabath, N.; Landan, G.; Graur, D. A method for the simultaneous estimation of selection intensities in overlapping genes. PLoS One 2008, 3, e3996.
23. Chen, W.-C.; Dorman, K.S. Twisted Sisters: Disentangling Selection in Overlapping Reading Frames. In Proceedings of the Joint Statistical Meetings, Washington, DC, USA, 4 August 2009.
24. Lee, J.H.; Murphy, S.C.; Belshan, M.; Sparks, W.O.; Wannemuehler, Y.; Liu, S.; Hope, T.J.; Dobbs, D.; Carpenter, S. Characterization of functional domains of equine infectious anemia virus Rev suggests a bipartite RNA-binding domain. J. Virol. 2006, 80, 3844-3852.
25. Fridell, R.A.; Partin, K.M.; Carpenter, S.; Cullen, B.R. Identification of the activation domain of equine infectious anemia virus Rev. J. Virol. 1993, 67, 7317-23.
26. Mancuso, V.A.; Hope, T.J.; Zhu, L.; Derse, D.; Phillips, T.; Parslow, T.G. Posttranscriptional effector domains in the Rev proteins of feline immunodeficiency virus and equine infectious anemia virus. J. Virol. 1994, 68, 1998-2001.
27. Harris, M.E.; Gontarek, R.R.; Derse, D.; Hope, T.J. Differential requirements for alternative splicing and nuclear export functions of equine infectious anemia virus Rev protein. Mol. Cell. Biol. 1998, 18, 3889-3899.
28. Iversen, A.K.N.; Shpaer, E.G.; Rodrigo, A.G.; Hirsch, M.S.; Walker, B.D.; Sheppard, H.W.; Merigan, T.C.; Mullins, J.I. Persistence of attenuated Rev genes in a human immunodeficiency virus type 1-infected asymptomatic individual. J. Virol. 1995, 69, 5743-5753.
29. Hua, J.; Caffrey, J.J.; Cullen, B.R. Functional consequences of natural sequence variation in the activation domain of HIV-1 Rev. Virology 1996, 222, 423-429.
30. Churchill, M.J.; Chiavaroli, L.; Wesselingh, S.L.; Gorry, P.R. Persistence of attenuated HIV-1 Rev alleles in an epidemiologically linked cohort of long-term survivors infected with nef-deleted virus. Retrovirology 2007, 4, 43.