Evolution of the MGMT gene in primates: from structure to mobile genetic elements

Keywords: primates, gene MGMT, primate-specific mobile genetic elements

Abstract

The article collects data on the evolution of the reparative MGMT gene in primates and traces the evolutionary fate of a number of mobile genetic elements (MGEs). It was concluded that the evolution of the MGMT gene in primates underwent various changes from acquisition to loss of exon/intron sequences. As for primate-specific MGEs, they have a different evolutionary history and path - from the formation of species/genus-specific sequences to deletional degradation and can be components not only of intronic or exonic sequences, but also components of exons in the form of fragmented sequences and not be identified as MGEs.

References

Baker J. N., Walker J. A., Vanchiere J. A., Phillippe K. R., St. Romain C.P., Gonzalez- Quiroga P., Denham M.W., Mierl J.R., Konkel M.K., Batzer M.A. Evolution of Alu subfamily structure in the Saimiri lineage of new world monkeys. Genome Biol. Evol. 2017. Vol. 9(9). P. 2365–2376. doi: 10.1093/gbe/evx172.

Bénit L., Calteau A., Heidmann T. Characterization of the low-copy HERV-Fc family: evidence for recent integrations in primates of lements with coding envelope genes. Virology. 2003. Vol. 312(1). P. 159-168.

Blomberg J., Benachenhou F., Blikstad V., Sperber G., Mayer J. Classification and nomenclature of endogenous retroviral sequences (ERVs): problems and recommendations. Gene. 2009. Vol. 448(2). P. 115-123. doi:10.1016/j.gene.2009.06.007.

Boissinot S., Chevret P., Furano A.V. L1 (LINE-1) retrotransposon evolution and amplification in recent human history. Mol. Biol. Evol. 2000. Vol. 17(6). P. 915-928.

Brouha B., Schustak J., Badge R.M., Lutz-Prigge S., Farley A.H., Moran J.V., Kazazian H.H. Jr. Hot L1s account for the bulk of retrotransposition in the human population. Proc. Natl. Acad. Sci. USA. 2003. Vol. 100(9). P. 5280-5285.

Cantrell M.A., Grahn R.A., Scott L., Wichman H.A. Isolation of markers from recently transposed LINE-1 retrotransposons. Biotechniques. 2000. Vol. 29(6). P. 1310-1316.

Chenais B., Caruso A., Hiard S., Casse N. The impact of transposable elements on eukaryotic genomes: from genome size increase to genetic adaptation to stressful environments. Gene. 2012. Vol. 509(1). P. 7-15. doi: 10.1016/j.gene.2012.07.042.

Deininger P. Alu elements: know the SINEs. Genome Biol. 2011. Vol.12(12). P. 236.

de Koning A.P., Gu W., Castoe T.A., Batzer M.A., Pollock D.D. Repetitive elements may comprise over two-thirds of the human genome. PLoS Genet. 2011. Vol. 7(12). e1002384. doi: 10.1371/journal.pgen.1002384.

Escalera-Zamudio M., Greenwood A.D. On the classification and evolution of endogenous retrovirus: human endogenous retroviruses may not be 'human' after all. APMIS. 2016. Vol. 124(1-2). P. 44-51. doi: 10.1111/apm.12489.

Furano A.V. The biological properties and evolutionary dynamics of mammalian LINE-1 retrotransposons. Prog. Nucleic Acid Res.Mol. Biol. 2000. Vol. 64. P. 255-294.

Gu Z., Wang H., Nekrutenko A., Li W.H. Densities, length proportions, and other distributional features of repetitive sequences in the human genome estimated from 430 megabases of genomic sequence. Gene. 2000. Vol. 259(1-2). P. 81-88.

Häsler J., Strub K. Alu elements as regulators of gene expression. Nucleic Acids Res. 2006. Vol. 34(19). P. 5491–5497. doi: 10.1093/nar/gkl706.

Kaina B., Christmann M., Naumann S., Roos W.P. MGMT: key node in the battle against genotoxicity, carcinogenicity and apoptosis induced by alkylating agents. DNA Repair (Amst). 2007. Vol. 8. Р. 1079–1099. doi:10.1016/j.dnarep.2007.03.008.

Kapitonov V., Jurka J. The age of Alu subfamilies. J. Mol. Evol. 1996. Vol. 429(1). P. 59- 65.

Kazazian H.H. J.r, Moran J.V. Mobile DNA in Health and Disease. N. Engl. J. Med. 2017. Vol. 377(4). P. 361-370. doi: 10.1056/NEJMra1510092.

Konkel M. K., Walker J. A., Batzer M. A. LINEs and SINEs of primate evolution. Evol. Anthropol. 2010. Vol. 19. P. 236–249.

Lander E., Linton L. M., Birren B., Nusbaum C., Zody M. et al. Initial sequencing and analysis of the human genome. Nature. 2001. 409(6822). P. 860–921.

Lee H.-E., Eo J., Kim H.-S. Composition and evolutionary importance of transposable elements in humans and primates. Genes Genomics. 2015. Vol. 37(2). P. 135–140.

Mager D.L., Stoye J.P. Mammalian Endogenous Retroviruses. Microbiol. Spectr. 2015. Vol. 3(1). MDNA3-0009-2014. doi: 10.1128/microbiolspec.MDNA3-0009-2014.

Margison G.P., Butt A., Pearson S.J., Wharton S., Watson A.J., Marriott A., Caetano C.M., Hollins J.J., Rukazenkova N., Begum G., Santibáñez-Koref M.F. Alkyltransferase-like Proteins. DNA Repair (Amst). 2007. Vol. 6.P.1222-1228. doi: 10.1016/j.dnarep.2007.03.014.

McLain A.T., Carman G.W., Fullerton M.L., Beckstrom T.O., Gensler W., Meyer T.J., Faulk C., Batzer M.A. Analysis of western lowland gorilla (Gorilla gorilla gorilla) specific Alu repeats. Mob. DNA. 2013. Vol. 4(1). P. 26. doi: 10.1186/1759-8753-4-26.

Mighell A.J., Markham A.F., Robinson P.A. Alu sequences. FEBS Lett. 1997. Vol. 417(1). P.1-5. doi: 10.1016/s0014-5793(97)01259-3.

Mills R.E., Bennett E.A., Iskow R.C., Devine S.E. Which transposable elements are active in the human genome? Trends Genet. 2007. Vol. 23(4). P. 183-191.

Pegg A.E. Repair of O6-alkylguanine by alkyltransferases. Mutat. Res. 2000. Vol. 262. P. 83-100.

Pegg A.E. Multifaceted roles of alkyltransferase and related proteins in DNA repair, DNA damage, resistance to chemotherapy, and research tools. Chem. Res. Toxicol. 2011. Vol. 24. P. 618-639. doi: 10.1021/tx200031q.

Perelman P., Johnson W.E., Roos C., Seuánez H.N., Horvath J.E., Moreira M.A., Kessing B., Pontius J., Roelke M., Rumpler Y., Schneider M.P., Silva A., O'Brien S.J., Pecon-Slattery J. A molecular phylogeny of living primates. PLoS Genet. 2011. Vol. 7(3). e1001342. doi: 10.1371/journal.pgen.1001342.

Pidpala O.V., Lukash L.L. Distribution of mobile genetic elements in the human O(6)-methylguanine-DNA methyltransferase gene. XII International Scientific and Practical Conference “Current problems of modern biology and human health”. 2012. Issue 12. P. 150-154. [in Ukrainian].

Pidpala O.V., Lukash L.L. Recombination origin of the nuclear introns. Factors Experimental Evol. Organisms. 2017. Vol. 20. P. 329-334. [in Ukrainian]. doi: 10.7124/FEEO.v20.789

Pidpala O.V., Lukash L.L. The analisis of human MGMT gene orthologous in Protists. Factors Experim. Evol. Organisms. 2018. Vol. 22. P. 345-351. [in Ukrainian]. doi: 10.7124/FEEO.v22.973

Pidpala O.V., Lukash L.L. Formation of the L1Hs retroelement in the intron of the MGMT gene of Hominoidea. Factors Experim. Evol. Organisms. 2019. Vol. 24. P. 338-344. [in Ukrainian]. doi: 10.7124/FEEO.v24.1126

Pidpala O.V., Lukash L.L. In silico analysis of MGMT gene orthologous in the most ancient Strepsirrhini primates. Factors Experim. Evol. Organisms. 2020. Vol. 26. P. 305-310. [in Ukrainian]. doi: 10.7124/FEEO.v26.1284

Pidpala O.V., Lukash L.L. Species-specific mobile genetic elements in the gene of repair enzyme MGMT in New World monkeys. Factors Experim. Evol. Organisms. 2021. Vol. 28. P. 128-134. [in Ukrainian]. doi: 10.7124/FEEO.v28.1388

Pidpala O.V., Lukash L.L. Evolutionary history of species-specific Alu repeats on the example of the MGMT gene of Old World monkey. Factors Experim. Evol. Organisms. 2021. Vol. 28. P. 128-134. [in Ukrainian]. doi: 10.7124/FEEO.v30.1473

Pidpala O.V., Lukash L.L. Distribution of the macaques genus-specific Alu repeat AluMacYa3 in the MGMT gene orthologs of Old World monkeys. Factors Experimental Evol. Organisms. 2023. Vol. 32. P. 148-154. [in Ukrainian]. doi: 10.7124/FEEO.v32.1552

Quentin Y. Origin of the Alu family: a family of Alu-like monomers gave birth to the left and the right arms of the Alu elements. Nucleic Acids Res. 1992. Vol. 20(13). P. 3397–3401.

Raaum R.L., Sterner K.N., Noviello C.M., Stewart C.B., Disotell T.R. Catarrhine primate divergence dates estimated from complete mitochondrial genomes: concordance with fossil and nuclear DNA evidence. J. Hum. Evol. 2005. Vol. 48. P. 237–257.

Salem A.H., Ray D.A., Xing J., Callinan P.A., Myers J.S., Hedges D.J., Garber R.K., Witherspoon D.J., Jorde L.B., Batzer M.A. Alu elements and hominid phylogenetics. Proc. Natl. Acad. Sci. USA.2003. Vol. 100(22).P.12787–12791. doi:10.1073/pnas.2133766100.

Schmitz J., Noll A., Raabe C.A., Churakov G., Voss R., Kiefmann M., Rozhdestvensky T., Brosius J., Baertsch R., Clawson H., Roos C., Zimin A., Minx P., Montague M.J., Wilson R.K., Warren W.C. Genome sequence of the basal haplorrhine primate Tarsius syrichta reveals unusual insertions. Nat.Commun.2016.Vol.7. P.12997. doi: 10.1038/ncomms12997.

Skowronski J., Fanning T.G., Singer M.F. Unit-length line-1 transcripts in human teratocarcinoma Cells. Mol. Cell. Biol. 1988. Vol. 8(4). P. 1385–1397.

Smit A.F., Tóth G., Riggs A.D., Jurka J. Ancestral, mammalian-wide subfamilies of LINE-1 repetitive sequences. J. Mol. Biol. 1995. Vol. 246(3). P. 401-417.

Sotero-Caio C.G., Platt R.N., Suh A., Ray D.A. Evolution and diversity of transposable elements in vertebrate genomes. Genome Biol. Evol. 2017. Vol. 9. P. 161-177. doi: 10.1093/gbe/evw264.

Ullu E., Tschudi C. Alu sequences are processed 7SL RNA genes. Nature. 1984. Vol. 312(5990). P. 171-172.

Vargiu L., Rodriguez-Tomé P., Sperber G.O., Cadeddu M., Grandi N., Blikstad V., Tramontano E., Blomberg J. Classification and characterization of human endogenous retroviruses: mosaic forms are common. Retrovirology. 2016. Vol. 13. P. 7. doi:10.1186/s12977-015-0232-y.