Evolution, And Phylogeny Of Herv-S Family In Some Closely Related Primates


Hawnaz Othman Najmalddin1, Aso Ahmed Taher1, and Shad Arif Mohammed1

1College of Science, University of Sulaimani.





Abstract
Human endogenous retroviral element S-family (HERV-S) has been present within
the human genome as well as various closely related primates. The expression
pattern, copy number, chromosomal locations of the proviral element have been
extensively studied. Here, we analyse the pol fragment of the HERV-S in human
tissues, cancer cell lines and in seven other related primates. Phylogenetic analysis of
the HERV-S pol gene suggests division of the family into two groups among the
tested species that have arisen throughout the primate evolution by gene duplication
as well as other genetic alterations. Also, the tree analysis of human tissues and
cancer cells suggest that expression of the chromosome X pol fragment is identical to
expression of the pol fragment in cancerous cells more than its relation to the pol
sequence on other human chromosomes. To sum up, our data provide a clarification
about the dynamic evolutionary characteristics as well as phylogenetic relationships
of HERV-S family pol gene in primates.

Key Words: HERV-S, Endogenous, Phylogeny, Evolution, Primate, Cancer cell line



References

1. ALTSCHUL, S. F., MADDEN, T. L., SCHÄFFER, A. A., ZHANG, J., ZHANG, Z., MILLER, W. &
LIPMAN, D. J. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs. Nucleic acids research, 25, 3389-3402.
2. BHARDWAJ, N. & COFFIN, J. M. 2014. Endogenous retroviruses and human cancer: is there anything to the
rumors? Cell host & microbe, 15, 255-259.
3. CHAKRABORTY, R. 1977. Estimation of time of divergence from phylogenetic studies. Canadian Journal of
Genetics and Cytology, 19, 217-223.
4. EDGAR, R. C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput.
Nucleic acids research, 32, 1792-1797.
5. FELSENSTEIN, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 783-
791.
6. FISCHER, S., ECHEVERRÍA, N., MORATORIO, G., LANDONI, A. I., DIGHIERO, G., CRISTINA, J.,
OPPEZZO, P. & MORENO, P. 2014. Human endogenous retrovirus np9 gene is over expressed in chronic
lymphocytic leukemia patients. Leukemia research reports, 3, 70-72.
7. FOLEY, B., LEITNER, T., APETREI, C., HAHN, B., MIZRACHI, I., MULLINS, J., RAMBAUT, A.,
WOLINSKY, S. & KORBER, B. 2013. HIV sequence compendium 2013. Theoretical Biology and Biophysics
Group, Los Alamos National Laboratory, Los Alamos, NM, LAUR, 13-26007.
8. JERN, P., SPERBER, G. O. & BLOMBERG, J. 2004. Definition and variation of human endogenous
retrovirus H. Virology, 327, 93-110.
9. JONES, D. T., TAYLOR, W. R. & THORNTON, J. M. 1992. The rapid generation of mutation data matrices
from protein sequences. Computer applications in the biosciences: CABIOS, 8, 275-282.
10. KIMURA, M. 1980. A simple method for estimating evolutionary rates of base substitutions through
comparative studies of nucleotide sequences. Journal of molecular evolution, 16, 111-120.

11. KJELLMAN, C., SJÖGREN, H.-O., SALFORD, L. G. & WIDEGREN, B. 1999. HERV-F (XA34) is a full-
length human endogenous retrovirus expressed in placental and fetal tissues. Gene, 239, 99-107.

12. KURTH, R. & BANNERT, N. 2010. Beneficial and detrimental effects of human endogenous retroviruses.
International journal of cancer, 126, 306-314.

13. LI, S., LIU, Z., YIN, S., CHEN, Y., YU, H., ZENG, J., ZHANG, Q. & ZHU, F. 2013. Human endogenous
retrovirus W family envelope gene activates the small conductance Ca 2+-activated K+ channel in human
neuroblastoma cells through CREB. Neuroscience, 247, 164-174.
14. ROMANISH, M., COHEN, C. & MAGER, D. Potential mechanisms of endogenous retroviral-mediated
genomic instability in human cancer. Seminars in cancer biology, 2010. Elsevier, 246-253.
15. SAITOU, N. & NEI, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic
trees. Molecular biology and evolution, 4, 406-425.
16. SHIMODAIRA, H. & HASEGAWA, M. 2001. CONSEL: for assessing the confidence of phylogenetic tree
selection. Bioinformatics, 17, 1246-1247.
17. TAJIMA, F. 1993. Simple methods for testing the molecular evolutionary clock hypothesis. Genetics, 135,
599-607.
18. TAMURA, K., BATTISTUZZI, F. U., BILLING-ROSS, P., MURILLO, O., FILIPSKI, A. & KUMAR, S.
2012. Estimating divergence times in large molecular phylogenies. Proceedings of the National Academy of
Sciences, 109, 19333-19338.
19. TAMURA, K., STECHER, G., PETERSON, D., FILIPSKI, A. & KUMAR, S. 2013. MEGA6: molecular
evolutionary genetics analysis version 6.0. Molecular biology and evolution, 30, 2725-2729.
20. TRISTEM, M. 2000. Identification and characterization of novel human endogenous retrovirus families by
phylogenetic screening of the human genome mapping project database. Journal of virology, 74, 3715-3730.
21. YI, J.-M., KIM, T.-H., HUH, J.-W., PARK, K. S., JANG, S. B., KIM, H.-M. & KIM, H.-S. 2004. Human
endogenous retroviral elements belonging to the HERV-S family from human tissues, cancer cells, and
primates: expression, structure, phylogeny and evolution. Gene, 342, 283-292.
22. ZUCKERKANDL, E. & PAULING, L. 1965. Evolutionary divergence and convergence in proteins. Evolving
genes and proteins, 97, 97-166.