Sequence polymorphisms in the long terminal repeat of bovine leukemia virus: Evidence for selection pressures in regulatory sequences

Virus Research

Volumn 124, Issue 1-2, 2007, Pages 113-124

  Zhao, Xiangrong ^a   Jimenez, Carlos ^b   Sentsui, Hiroshi ^c   Buehring, Gertrude C ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSIDAD NACIONAL   (Costa Rica)

^c NIHON UNIVERSITY   (Japan)

Author keywords

Bovine leukemia virus; Long terminal repeat; Phylogeny; Polymorphisms; Selection

Indexed keywords

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; BOVINE LEUKEMIA VIRUS; CATTLE; GENETIC POLYMORPHISM; GEOGRAPHIC DISTRIBUTION; LONG TERMINAL REPEAT; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; REGULATORY SEQUENCE; VIRUS ISOLATION;

5' UNTRANSLATED REGIONS; ANIMALS; BASE SEQUENCE; CATTLE; ENZOOTIC BOVINE LEUKOSIS; GENOME, VIRAL; GEOGRAPHY; LEUKEMIA VIRUS, BOVINE; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMORPHISM, GENETIC; REGULATORY SEQUENCES, NUCLEIC ACID; SELECTION (GENETICS); SEQUENCE HOMOLOGY, NUCLEIC ACID; TERMINAL REPEAT SEQUENCES;

BOS; BOVINE LEUKEMIA VIRUS; DELTARETROVIRUS; RETROVIRIDAE; SIMIAN T-LYMPHOTROPIC VIRUS 3;

EID: 33846834114     PISSN: 01681702     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.virusres.2006.10.010     Document Type: Article

References (56)

1. Alexandersen S., Carpenter S., Christensen J., Storgaard T., Viuff B., Wannemuehler Y., Belousov J., and Roth J.A. Identification of alternatively spliced mRNAs encoding potential new regulatory proteins in cattle infected with bovine leukemia virus. J. Virol. 67 (1993) 39-52
2. Asfaw Y., Tsuduku S., Konishi M., Murakami K., Tsuboi T., Wu D., and Sentsui H. Distribution and superinfection of bovine leukemia virus genotypes in Japan. Arch. Virol. 150 (2005) 493-505
3. Ball J.K., Diggelmann H., Dekaban G.A., Grossi G.F., Semmler R., Waight P.A., and Fletcher R.F. Alterations in the U3 region of the long terminal repeat of an infectious thymotropic type B retrovirus. J. Virol. 62 (1988) 2985-2993
4. Bhadra S., Lozano M.M., and Dudley J.P. Conversion of mouse mammary tumor virus to a lymphomagenic virus. J. Virol. 79 (2005) 12592-12596
5. Beier D., Blankenstein P., Marquardt O., and Kuzmak J. Identification of different BLV provirus isolates by PCR, RFLPA, and DNA sequencing. Muench. Tieraerztl. Wschr. 114 (2001) 252-256
6. Biek R., Rodrigo A.G., Holley D., Drummond A., Anderson Jr. C.R., Ross H.A., and Poss M. Epidemiology, genetic diversity, and evolution of endemic feline immunodeficiency virus in a population of wild cougars. J. Virol. 77 (2003) 9578-9589
7. Blackard J.T., Renjifo B., Chaplin B., Msamanga G., Fawzi W., and Essex M. Diversity of the HIV-1 long terminal repeat following mother-to-child transmission. Virology 274 (2000) 402-411
8. Brooks P.A., Nyborg J.K., and Cockerell G.L. Identification of an NF-kappa B binding site in the bovine leukemia virus promoter. J. Virol. 69 (1995) 6005-6009
9. Brooks P.A., Cockerell G.L., and Nyborg J.K. Activation of BLV transcription by NF-kappa B and Tax. Virology 243 (1998) 94-98
10. Calomme C., Nguyen T.L., de Launoit Y., Kiermer V., Droogmans L., Burny A., and Van Lint C. Upstream stimulatory factors binding to an E box motif in the R region of the bovine leukemia virus long terminal repeat stimulates viral gene expression. J. Biol. Chem. 277 (2002) 8775-8789
11. Calomme C., Dekoninck A., Nizet S., Adam E., Nguyen T.L., Van Den Broeke A., Willems L., Kettmann R., Burny A., and Van Lint C. Overlapping CRE and E box motifs in the enhancer sequences of the bovine leukemia virus 5′ long terminal repeat are critical for basal and acetylation-dependent transcriptional activity of the viral promoter: implications for viral latency. J. Virol. 78 (2004) 13848-13864
12. Camargos M.F., Stancek D., Rocha M.A., Lessa L.M., Reis J.K.P., and Leite R.C. Partial sequencing of env gene of bovine leukemia virus from Brazilian samples and phylogenetic analysis. J. Vet. Med. B 49 (2002) 325-330
13. Chandler V.L., Maler B.A., and Yamamoto K.R. DNA sequences bound specifically by glucocorticoid receptor in vitro render a heterologous promoter hormone responsive in vivo. Cell 33 (1983) 489-499
14. Coulston J., Naif H., Brandon R., Kumar S., Khan S., Daniel R.C., and Lavin M.F. Molecular cloning and sequencing of an Australian isolate of proviral bovine leukaemia virus DNA: comparison with other isolates. J. Gen. Virol. 71 (1990) 1737-1746
15. Dekoninck A., Calomme C., Nizet S., de Launoit Y., Burny A., Ghysdael J., and Van Lint C. Identification and characterization of a PU.1/Spi-B binding site in the bovine leukemia virus long terminal repeat. Oncogene 22 (2003) 2882-2896
16. Derse D., and Casey J.W. Two elements in the bovine leukemia virus long terminal repeat that regulate gene expression. Science 231 (1986) 1437-1440
17. Derse D. Bovine leukemia virus transcription is controlled by a virus-encoded trans-acting factor and by cis-acting response elements. J. Virol. 61 (1987) 2462-2471
18. Deutsch P.J., Hoeffler J.P., Jameson J.L., and Habener J.F. Cyclic AMP and phorbol ester-stimulated transcription mediated by similar DNA elements that bind distinct proteins. Proc. Natl. Acad. Sci. U.S.A. 85 (1988) 7922-7926
19. Dube S., Dolcini G., Abbott L., Mehta S., Dube D., Gutierrez S., Ceriani C., Esteban E., Ferrer J., and Poiesz B. The complete genomic sequence of a BLV strain from a Holstein cow from Argentina. Virology 277 (2000) 379-386
20. Eiraku N., Monken C., Kubo T., Zhu S.W., Rios M., Bianco C., Hjelle B., Nagashima K., and Hall W. Nucleotide sequence and restriction fragment length polymorphism analysis of the long terminal repeat of human T cell leukemia virus type II. AIDS Res. Hum. Retroviruses 11 (1995) 625-636
21. Fechner H., Blankenstein P., Looman A.C., Elwert J., Geue L., Albrecht C., Krug A., Beier D., Marquardt O., and Ebner D. Provirus variants of the bovine leukemia virus and their relation to the serological status of naturally infected cattle. Virology 237 (1997) 261-269
22. Felsenstein, J., 2004. PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.
23. Graves D.C., and Ferrer J.F. In vitro transmission and propagation of the bovine leukemia virus in monolayer cell cultures. Cancer Res. 36 (1976) 4152-4159
24. Hernandez N. TBP, a universal eukaryotic transcription factor?. Genes Dev. 7 (1993) 1291-1308
25. Ibanez A., Clotet B., and Martinez M.A. Absence of genetic diversity reduction in the HIV-1 integrated proviral LTR sequence population during successful combination therapy. Virology 282 (2001) 1-5
26. Jeeninga R.E., Hoogenkamp M., Armand-Ugon M., de Baar M., Verhoef K., and Berkhout B. Functional differences between the long terminal repeat transcriptional promoters of human immunodeficiency virus type 1 subtypes A through G. J. Virol. 74 (2000) 3740-3751
27. Katoh I., Yoshinaka Y., and Ikawa Y. Bovine leukemia virus trans-activator p38tax activates heterologous promoters with a common sequence known as a cAMP-responsive element or the binding site of a cellular transcription factor ATF. EMBO J. 8 (1989) 497-503
28. Kerkhofs P., Heremans H., Burny A., Kettmann R., and Willems L. In vitro and in vivo oncogenic potential of bovine leukemia virus G4 protein. J. Virol. 72 (1998) 2554-2559
29. Kiermer V., Van Lint C., Briclet D., Vanhulle C., Kettmann R., Verdin E., Burny A., and Droogmans L. An interferon regulatory factor binding site in the U5 region of the bovine leukemia virus long terminal repeat stimulates Tax-independent gene expression. J. Virol. 72 (1998) 5526-5534
30. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16 (1980) 111-120
31. Komurian F., Pelloquin F., and de The G. In vivo genomic variability of human T-cell leukemia virus type I depends more upon geography than upon pathologies. J. Virol. 65 (1991) 3770-3778
32. Kumar S., Tamura K., and Nei M. MEGA 3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinform. 5 (2004) 150-163
33. Licursi M., Inoshima Y., Wu D., Yokoyama T., Gonzalez E.T., and Sentsui H. Provirus variants of bovine leukemia virus in naturally infected cattle from Argentina and Japan. Vet. Microbiol. 96 (2003) 17-23
34. Mansky L.M., and Temin H.M. Lower mutation rate of bovine leukemia virus relative to that of spleen necrosis virus. J. Virol. 68 (1994) 494-499
35. Mansky L.M. Retrovirus mutation rates and their role in genetic variation. J. Gen. Virol. 79 (1998) 1337-1345
36. Mamoun R.Z., Morissonm M., Rebeyrotte N., Busetta B., Couez D., Kettmann R., Hospital M., and Guillemain B. Sequence variability of bovine leukemia virus env gene and its relevance to the structure and antigenicity of the glycoproteins. J. Virol. 64 (1990) 4180-4188
37. McGirr K.M., and Buehring G.C. Tax and rex sequences of bovine leukaemia virus from globally diverse isolates: rex amino acid sequence more variable than tax. J. Vet. Med. B 52 (2005) 8-16
38. Merezak C., Pierreux C., Adam E., Lemaigre F., Rousseau G.G., Calomme C., Van Lint C., Christophe D., Kerkhofs P., Burny A., Kettmann R., and Willems L. Suboptimal enhancer sequences are required for efficient bovine leukemia virus propagation in vivo: implications for viral latency. J. Virol. 75 (2001) 6977-6988
39. Miller V. Commentary: sifting through the maze of viral and host diversity and HIV/AIDS clinical progression. Int. J. Epidemiol. 34 (2005) 584-585
40. Monti G., Schrijver R., and Beier D. Genetic diversity and spread of bovine leukaemia virus isolates in Argentine dairy cattle. Arch. Virol. 150 (2005) 443-458
41. NAHMS, 1997a. http://www.aphis.usda.gov/vs/ceah/ncahs/nahms/dairy/dairy96/DR96digderm.pdf.
42. NAHMS, 1997b. http://www.aphis.usda.gov/vs/ceah/ncahs/nahms/beefcowcalf/beef97/bf97obj.htm.
43. Niermann G.L., and Buehring G.C. Hormone regulation of bovine leukemia virus via the long terminal repeat. Virology 239 (1997) 249-258
44. Pistello M., Del Santo B., Butto S., Bargagna M., Domenici R., and Bendinelli M. Genetic and phylogenetic analyses of HIV-1 corroborate the transmission link hypothesis. J. Clin. Virol. 30 (2004) 11-18
45. Ramirez E., Cartier L., Villota C., and Fernandez J. Genetic characterization and phylogeny of human T-cell lymphotropic virus type I from Chile. Virus Res. 84 (2002) 135-149
46. Roberts J.D., Bebenek K., and Kunkel T.A. The accuracy of reverse transcriptase from HIV-1. Science 242 (1988) 1171-1173
47. Rozas J., Sanchez-DelBarrio J.C., Messeguer X., and Rozas R. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19 (2003) 2496-2497
48. Sagata N., Yasunaga T., Tsuzuku-Kawamura J., Ohishi K., Ogawa Y., and Ikawa Y. Complete nucleotide sequence of the genome of bovine leukemia virus: its evolutionary relationship to other retroviruses. Proc. Natl. Acad. Sci. U.S.A. 82 (1985) 677-681
49. Seibert S.A., Howell C.Y., Hughes M.K., and Hughes A.L. Natural selection on the gag, pol, and env genes of human immunodeficiency virus (HIV-1). Mol. Biol. Evol. 12 (1995) 803-813
50. Troyer R.M., Collins K.R., Abraha A., Fraundorf E., Moore D.M., Krizan R.W., Toossi Z., Colebunders R.L., Jensen M.A., Mullins J.I., Vanham G., and Arts E.J. Changes in human immunodeficiency virus type 1 fitness and genetic diversity during disease progression. J. Virol. 79 (2005) 9006-9018
51. Van Der Maaten M.J., and Miller J.M. Replication of bovine leukemia virus in monolayer cell cultures. Bibl. Haematol. 43 (1975) 360-362
52. Weaver E.A., Collisson E.W., Slater M., and Zhu G. Phylogenetic analyses of Texas isolates indicate an evolving subtype of the clade B feline immunodeficiency viruses. J. Virol. 78 (2004) 2158-2163
53. Willems L., Thienpont E., Kerkhofs P., Burny A., Mammerickx M., and Kettmann R. Bovine leukemia virus, an animal model for the study of intrastrain variability. J. Virol. 67 (1993) 1086-1089
54. Willems L., Kerkhofs P., Dequiedt F., Portetelle D., Mammerickx M., Burny A., and Kettmann R. Attenuation of bovine leukemia virus by deletion of R3 and G4 open reading frames. Proc. Natl. Acad. Sci. U.S.A. 91 (1994) 11532-11536
55. Willems L., Kerkhofs P., Burny A., Mammerickx M., and Kettmann R. Lack of LTR and ENV genetic variation during bovine leukemia virus-induced leukemogenesis. Virology 206 (1995) 769-772
56. Xiao J., and Buehring G.C. In vivo protein binding and functional analysis of cis-acting elements in the U3 region of the bovine leukemia virus long terminal repeat. J. Virol. 72 (1998) 5994-6003