Cross-sectional dating of novel haplotypes of HERV-K 113 and HERV-K 115 indicate these proviruses originated in Africa before Homo sapiens

Molecular Biology and Evolution

Volumn 26, Issue 11, 2009, Pages 2617-2626

  Jha, Aashish R ^a,b   Pillai, Satish K ^c   York, Vanessa A ^a   Sharp, Elizabeth R ^a   Storm, Emily C ^a   Wachter, Douglas J ^a   Martin, Jeffrey N ^d   Deeks, Steven G ^d   Rosenberg, Michael G ^e   Nixon, Douglas F ^a   Garrison, Keith E ^a,f  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CHICAGO   (United States)

^c SAN FRANCISCO VETERANS AFFAIRS MEDICAL CENTER   (United States)

^d SAN FRANCISCO GENERAL HOSPITAL   (United States)

^e ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

^f SAINT MARY'S COLLEGE OF CALIFORNIA   (United States)

Author keywords

Haplotype; HERV K113 and HERV K115; Hervotype; Homo erectus; Human evolution; Insertion frequencies

Indexed keywords

AFRICA; AFRICAN AMERICAN; ARTICLE; CAUCASIAN; CONTROLLED STUDY; CROSS-SECTIONAL STUDY; GENE FREQUENCY; GENE INSERTION; GENE SEQUENCE; GENETIC DISTANCE; GEOGRAPHIC DISTRIBUTION; HAPLOTYPE; HISPANIC; HUMAN; HUMAN ENDOGENOUS RETROVIRUS; HUMAN GENOME; HUMAN IMMUNODEFICIENCY VIRUS 1; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; LONG TERMINAL REPEAT; NUCLEOTIDE SEQUENCE; PROVIRUS; RETROVIRUS; SINGLE NUCLEOTIDE POLYMORPHISM; UNITED STATES; VIRUS STRAIN; CLASSIFICATION; ENDOGENOUS RETROVIRUS; GENE EXPRESSION REGULATION; GENETICS; MOLECULAR EVOLUTION; VIRUS GENOME;

HOMO ERECTUS; HOMO SAPIENS; HUMAN ENDOGENOUS RETROVIRUSES; HUMAN IMMUNODEFICIENCY VIRUS 1;

AFRICA; ENDOGENOUS RETROVIRUSES; EVOLUTION, MOLECULAR; GENOME, VIRAL; HAPLOTYPES; HUMANS; MUTAGENESIS, INSERTIONAL;

EID: 72849121671     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msp180     Document Type: Article

References (48)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol. 215:403-410.
2. Bannert N, Kurth R. 2004. Retroelements and the human genome: new perspectives on an old relation. Proc Natl Acad Sci USA. 101(Suppl 2):14572-14579.
3. Bannert N, Kurth R. 2006. The evolutionary dynamics of human endogenous retroviral families. Annu Rev Genomics Hum Genet. 7:149-173.
4. Barbulescu M, Turner G, Seaman MI, Deinard AS, Kidd KK, Lenz J. 1999. Many human endogenous retrovirus K (HERV-K) proviruses are unique to humans. Curr Biol. 9:861-868. (Pubitemid 29456003)
5. Belshaw R, Dawson AL, Woolven-Allen J, Redding J, Burt A, Tristem M. 2005. Genomewide screening reveals high levels of insertional polymorphism in the human endogenous retrovirus family HERV-K(HML2): implications for present-day activity. J Virol. 79:12507-12514.
6. Belshaw R, Watson J, Katzourakis A, Howe A, Woolven-Allen J, Burt A, Tristem M. 2007. Rate of recombinational deletion among human endogenous retroviruses. J Virol. 81:9437-9442. (Pubitemid 47311486)
7. Bulmer M, Wolfe KH, Sharp PM. 1991. Synonymous nucleotide substitution rates in mammalian genes: implications for the molecular clock and the relationship of mammalian orders. Proc Natl Acad Sci USA. 88:5974-5978.
8. Burmeister T, Ebert AD, Pritze W, Loddenkemper C, Schwartz S, Thiel E. 2004. Insertional polymorphisms of endogenous HERV-K113 and HERV-K115 retroviruses in breast cancer patients and age-matched controls. AIDS Res Hum Retroviruses. 20:1223-1229.
9. Clark JD, de Heinzelin J, Schick KD, et al. (11 co-authors). 1994. African Homo erectus: old radiometric ages and young Oldowan assemblages in the Middle Awash Valley, Ethiopia. Science. 264:1907-1910.
10. Contreras-Galindo R, Kaplan MH, Leissner P, et al. (11 co-authors). 2008. Human endogenous retrovirus-K (HML-2) elements in the plasma of people with lymphoma and breast cancer. J Virol. 82:9329-9336.
11. Contreras-Galindo R, Lopez P, Velez R, Yamamura Y. 2007. HIV-1 infection increases the expression of human endogenous retroviruses type K (HERV-K) in vitro. AIDS Res Hum Retroviruses. 23:116-122.
12. Corpet F. 1988. Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res. 16:10881-10890.
13. Costas J. 2001. Evolutionary dynamics of the human endogenous retrovirus family HERV-K inferred from full-length proviral genomes. J Mol Evol. 53:237-243.
14. Dangel AW, Baker BJ, Mendoza AR, Yu CY. 1995. Complement component C4 gene intron 9 as a phylogenetic marker for primates: long terminal repeats of the endogenous retrovirus ERV-K (C4) are a molecular clock of evolution. Immunogenetics. 42:41-52.
15. Ehlhardt S, Seifert M, Schneider J, Ojak A, Zang KD, Mehraein Y. 2006. Human endogenous retrovirus HERV-K(HML-2) Rec expression and transcriptional activities in normal and rheumatoid arthritis synovia. J Rheumatol. 33:16-23.
16. Garrison KE, Jones RB, Meiklejohn DA, et al. (14 co-authors). 2007. T cell responses to human endogenous retroviruses in HIV-1 infection. PLoS Pathog. 3:e165.
17. Gifford R, Tristem M. 2003. The evolution, distribution and diversity of endogenous retroviruses. Virus Genes. 26:291-315.
18. Golan M, Hizi A, Resau JH, Yaal-Hahoshen N, Reichman H, Keydar I, Tsarfaty I. 2008. Human endogenous retrovirus (HERV-K) reverse transcriptase as a breast cancer prognostic marker. Neoplasia. 10:521-533.
19. Herrera RJ, Lowery RK, Alfonso A, McDonald JF, Luis JR. 2006. Ancient retroviral insertions among human populations. J Hum Genet. 51:353-362.
20. Ho SY, Endicott P. 2008. The crucial role of calibration in molecular date estimates for the peopling of the Americas. Am J Hum Genet. 83:142-146.
21. Hughes JF, Coffin JM. 2004. Human endogenous retrovirus K solo-LTR formation and insertional polymorphisms: implications for human and viral evolution. Proc Natl Acad Sci USA. 101:1668-1672.
22. Johnson WE, Coffin JM. 1999. Constructing primate phylogenies from ancient retrovirus sequences. Proc Natl Acad Sci USA. 96:10254-10260.
23. Katzourakis A, Pereira V, Tristem M. 2007. Effects of recombination rate on human endogenous retrovirus fixation and persistence. J Virol. 81:10712-10717.
24. Kumar S, Subramanian S. 2002. Mutation rates in mammalian genomes. Proc Natl Acad Sci USA. 99:803-808.
25. Kimura M. 1968. Evolutionary rate at the molecular level. Nature. 217:624-626.
26. Lander ES, Linton LM, Birren B, et al. (255 co-authors). 2001. Initial sequencing and analysis of the human genome. Nature. 409:860-921.
27. Lavie L, Medstrand P, Schempp W, Meese E, Mayer J. 2004. Human endogenous retrovirus family HERV-K(HML-5): status, evolution, and reconstruction of an ancient betaretro-virus in the human genome. J Virol. 78:8788-8798
28. Lebedev YB, Belonovitch OS, Zybrova NV, Khil PP, Kurdyukov SG, Vinogradova TV, Hunsmann G, Sverdlov ED. 2000. Differences in HERV-K LTR insertions in orthologous loci of humans and great apes. Gene. 247:265-277.
29. Lower R. 1999. The pathogenic potential of endogenous retroviruses: facts and fantasies. Trends Microbiol. 7: 350-356.
30. Macfarlane C, Simmonds P. 2004. Allelic variation of HERV-K (HML-2) endogenous retroviral elements in human populations. J Mol Evol. 59:642-656.
31. Marguerat S, Wang WY, Todd JA, Conrad B. 2004. Association of human endogenous retrovirus K-18 polymorphisms with type 1 diabetes. Diabetes. 53:852-854.
32. Mariani-Costantini R, Horn TM, Callahan R. 1989. Ancestry of a human endogenous retrovirus family. J Virol. 63: 4982-4985.
33. Mayer J, Stuhr T, Reus K, Maldener E, Kitova M, Asmus F, Meese E. 2005. Haplotype analysis of the human endogenous retrovirus locus HERV-K (HML-2.HOM) and its evolutionary implications. J Mol Evol. 61:706-715.
34. McDougall I, Brown FH, Fleagle JG. 2005. Stratigraphic placement and age of modern humans from Kibish, Ethiopia. Nature. 433:733-736.
35. Moyes DL, Martin A, Sawcer S, Temperton N, Worthington J, Griffiths DJ, Venables PJ. 2005. The distribution of the endogenous retroviruses HERV-K113 and HERV-K115 in health and disease. Genomics. 86:337-341.
36. Noonan JP, Coop G, Kudaravalli S, et al. (11 co-authors). 2006. Sequencing and analysis of Neanderthal genomic DNA. Science. 314:1113-1118.
37. Otowa T, Tochigi M, Rogers M, Umekage T, Kato N, Sasaki T. 2006. Insertional polymorphism of endogenous retro-virus HERV-K115 in schizophrenia. Neurosci Lett. 408:226-229.
38. Pond SL, Frost SD. 2005. A simple hierarchical approach to modeling distributions of substitution rates. Mol Biol Evol. 22:223-234.
39. Pond SL, Frost SD, Muse SV. 2005. HyPhy: hypothesis testing using phylogenies. Bioinformatics. 21:676-679.
40. Reus K, Mayer J, Sauter M, Zischler H, Muller-Lantzsch N, Meese E. 2001. HERV-K(OLD): ancestor sequences of the human endogenous retrovirus family HERV-K(HML-2). J Virol. 75:8917-8926.
41. Rambaut A. 1996. Se-Al: sequence alignment editor v2.0 [Internet]. [cited 2005 March 1]; Available from: http://evolve.zoo.ox.ac.uk/
42. Rozen S, Skaletsky H. 2000. Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol. 132:365-386.
43. Sicat J, Sutkowski N, Huber BT. 2005. Expression of human endogenous retrovirus HERV-K18 superantigen is elevated in juvenile rheumatoid arthritis. J Rheumatol. 32:1821-1831.
44. Simpson GR, Patience C, Lower R, Tonjes RR, Moore HD, Weiss RA, Boyd MT. 1996. Endogenous D-type (HERV-K) related sequences are packaged into retroviral particles in the placenta and possess open reading frames for reverse transcriptase. Virology. 222:451-456.
45. Steinhuber S, Brack M, Hunsmann G, Schwelberger H, Dierich MP, Vogetseder W. 1995. Distribution of human endogenous retrovirus HERV-K genomes in humans and different primates. Hum Genet. 96:188-192.
46. Turner G, Barbulescu M, Su M, Jensen-Seaman MI, Kidd KK, Lenz J. 2001. Insertional polymorphisms of full-length endogenous retroviruses in humans. Curr Biol. 11: 1531-1535.
47. Wang-Johanning F, Radvanyi L, Rycaj K, Plummer JB, Yan P, Sastry KJ, Piyathilake CJ, Hunt KK, Johanning GL. 2008. Human endogenous retrovirus K triggers an antigen-specific immune response in breast cancer patients. Cancer Res. 68:5869-5877.
48. White TD, Asfaw B, DeGusta D, Gilbert H, Richards GD, Suwa G, Howell FC. 2003. Pleistocene Homo sapiens from Middle Awash, Ethiopia. Nature. 423:742-747.