Molecular Domestication of TLEWI DNA Transposons: Evidence and Contradictions

Мұқаба

Дәйексөз келтіру

Толық мәтін

Ашық рұқсат Ашық рұқсат
Рұқсат жабық Рұқсат берілді
Рұқсат жабық Тек жазылушылар үшін

Аннотация

Transposable elements (TE) are found in the genomes of almost all eukaryotes. They have a characteristic structure that ensures their transposition activity, as a result of which TE can make changes in the structure and functioning of the genome. Through coevolution with the genome, TE sequences can be domesticated. “Molecular domestication” refers to the co-optation of TE sequence, resulting in it becoming a functional part of the host genome. In bivalves, DNA transposons of the TLEWI subfamily have been identified, which have signs of domestication, as well as spliceosomal introns, which makes them similar to eukaryotic genes. To test the domestication hypothesis, this work carried out an intraspecific analysis of the presence of TLEWI transposons in the Pacific oyster (Crassostrea gigas) and their transcriptional activity in various tissues, during ontogeny and under the influence of internal and external factors. As a result, intraspecific heterogeneity was revealed in the presence of potentially functional copies and expression of transposase genes. For example, for two elements, a dependence of transcriptional activity on the stages of ontogenesis, as well as on temperature, was revealed. This suggests that functional (possibly domesticated) alleles have been conserved in distinct populations of the Pacific oyster. The accumulation of additional data will allow us to discover populations that retain active TLEWI transposase genes and to determine whether these genes have been domesticated by genome.

Толық мәтін

Рұқсат жабық

Авторлар туралы

M. Puzakov

Kovalevsky Institute of Biology of the Southern Seas, Russian Akademy of Sciences

Хат алмасуға жауапты Автор.
Email: puzakov.mikh@yandex.ru
Ресей, Sevastopol, 299011

L. Puzakova

Kovalevsky Institute of Biology of the Southern Seas, Russian Akademy of Sciences

Email: puzakov.mikh@yandex.ru
Ресей, Sevastopol, 299011

Y. Ulupova

Kovalevsky Institute of Biology of the Southern Seas, Russian Akademy of Sciences

Email: puzakov.mikh@yandex.ru
Ресей, Sevastopol, 299011

Әдебиет тізімі

  1. Bourque G., Burns K. H., Gehring M. et al. Ten things you should know about transposable elements // Genome Biology. 2018. V. 19. № 1. P. 199. doi: 10.1186/s13059-018-1577-z
  2. Kojima K.K. Structural and sequence diversity of eukaryotic transposable elements // Genes Genet. Syst. 2020. V. 94. P. 233–252. doi: 10.1266/ggs.18-00024
  3. Wells J.N., Feschotte C. A field guide to eukaryotic transposable elements // Annu. Rev. Genet. 2020. V. 23. № 54. P. 539–561. doi: 10.1146/annurev-genet-040620-022145
  4. Wallau G.L., Ortiz M.F., Loreto E.L. Horizontal transposon transfer in eukarya: Detection, bias, and perspectives // Genome Biol. Evol. 2012. V. 4. № 8. P. 689–699. doi: 10.1093/gbe/evs055
  5. Casacuberta E., González J. The impact of transposable elements in environmental adaptation // Mol. Ecol. 2013. V. 22. № 6. P. 1503–1517. doi: 10.1111/mec.12170
  6. Piacentini L., Fanti L., Specchia V. et al. Transposons, environmental changes, and heritable induced phenotypic variability // Chromosoma. 2014. V. 123. № 4. P. 345–354. doi: 10.1007/s00412-014-0464-y
  7. Auvinet J., Graça P., Belkadi L. et al. Mobilization of retrotransposons as a cause of chromosomal diversification and rapid speciation: The case for the Antarctic teleost genus Trematomus // BMC Genomics. 2018. V. 19. № 1. P. 339. doi: 10.1186/s12864-018-4714-x
  8. Jangam D., Feschotte C., Betrán E. Transposable element domestication as an adaptation to evolutionary conflicts // Trends Genet. 2017. V. 33. № 11. P. 817–831. doi: 10.1016/j.tig.2017.07.011
  9. Bowen N.J., Jordan I.K. Exaptation of protein coding sequences from transposable elements // Genome Dyn. 2007. V. 3. P. 147–162. doi: 10.1159/000107609
  10. Feschotte C., Pritham E. J. DNA transposons and the evolution of eukaryotic genomes // Annu. Rev. Genet. 2007. V. 41. P. 331–368. doi: 10.1146/annurev.genet.40.110405.090448
  11. Sinzelle L., Izsvák Z., Ivics Z. Molecular domestication of transposable elements: From detrimental parasites to useful host genes // Cell. Mol. Life Sci. 2009. V. 66 № 6. P. 1073–1093. doi: 10.1007/s00018-009-8376-3
  12. Kapitonov V.V., Jurka J. RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons // PLoS Biol. 2005. V. 3. № 6. doi: 10.1371/journal.pbio.0030181
  13. Panchin Y., Moroz L.L. Molluscan mobile elements similar to the vertebrate Recombination-Activating Genes // Biochem. Biophys. Res. Commun. 2008. V. 369. № 3. P. 818-823. doi: 10.1016/j.bbrc.2008.02.097
  14. Kim H.S, Chen Q., Kim S.K. et al. The DDN catalytic motif is required for Metnase functions in non-homologous end joining (NHEJ) repair and replication restart // J. Biol. Chem. 2014. V. 289. № 15. P. 10930–10938. doi: 10.1074/jbc.M113.533216
  15. Mateo L., González J. Pogo-like transposases have been repeatedly domesticated into CENP-B-related proteins // Genome Biol. Evol. 2014. V. 6. № 8. P. 2008–2016. doi: 10.1093/gbe/evu153
  16. Puzakov M.V., Puzakova L.V., Cheresiz S.V. The Tc1-like elements with the spliceosomal introns in mollusk genomes // Mol. Genet. and Genomics. 2020. V. 295. № 3. P. 621–633. doi: 10.1007/s00438-020-01645-1
  17. Altschul S.F., Madden T.L, Schäffer A.A. et al. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs // Nucl. Ac. Res. 1997. V. 25. № 17. doi: 10.1093/nar/25.17.3389
  18. Yamada K.D, Tomii K., Katoh K. Application of the MAFFT sequence alignment program to large data-reexamination of the usefulness of chained guide trees // Bioinformatics. 2016. V. 32. № 21. P. 3246–3251. doi: 10.1093/bioinformatics/btw412
  19. Nguyen L.T, Schmidt H.A, von Haeseler A., Minh B.Q. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies // Mol. Biol. Evol. 2015. V. 32. № 1. P. 268–274. doi: 10.1093/molbev/msu300
  20. Hoang D.T., Chernomor O., von Haeseler A. et al. UFBoot2: Improving the ultrafast bootstrap approximation // Mol. Biol. Evol. 2018. V. 35. № 2. P. 518–522. doi: 10.1093/molbev/msx281
  21. Kalyaanamoorthy S., Minh B.Q., Wong T.K.F. et al. ModelFinder: Fast model selection for accurate phylogenetic estimates // Nat. Methods. 2017. V. 14. № 6. P. 587–589. doi: 10.1038/nmeth.4285
  22. Bray N.L, Pimentel H., Melsted P., Pachter L. Near-optimal probabilistic RNA- seq quantification // Nat. Biotechnol. 2016. V. 34. № 5. P. 525–527. doi: 10.1038/nbt.3519
  23. Schaack S., Gilbert C., Feschotte C. Promiscuous DNA: horizontal transfer of transposable elements and why it matters for eukaryotic evolution // Trends Ecol. Evol. 2010. V. 25. № 9. P. 537–546. doi: 10.1016/j.tree.2010.06.001
  24. Blumenstiel J.P. Birth, school, work, death, and resurrection: The life stages and dynamics of transposable element proliferation // Genes (Basel). 2019. V. 10. № 5. P. 336. doi: 10.3390/genes10050336
  25. Puzakov M.V, Puzakova L.V, Cheresiz S.V. An analysis of IS630/Tc1/mariner transposons in the genome of a Pacific oyster, Crassostrea gigas // J. Mol. Evol. 2018. V. 86. P. 566–580. doi: 10.1007/s00239-018-9868-2
  26. Чересиз С.В., Юрченко Н.Н., Иванников А.В., Захаров И.К. Мобильные элементы и стресс // Информ. вестник ВОГиС. 2008. Т. 12. №. 1–2. С. 217–242.
  27. Юрченко Н.Н., Коваленко Л.В., Захаров И.К. Мобильные генетические элементы: нестабильность генов и геномов // Вавил. журн. генет. и селекции. 2011. Т. 15. №. 2. С. 261–270.
  28. Piacentini L, Fanti L, Specchia V. et al. Transposons, environmental changes, and heritable induced phenotypic variability // Chromosoma. 2014. V. 123. P. 345–354. doi: 10.1007/s00412-014-0464-y
  29. Grow E.J., Flynn R.A., Chavez S.L. et al. Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells // Nature. 2015. V. 522. P. 221–225. doi: 10.1038/nature14308
  30. Grundy E.E., Diab N., Chiappinelli K.B. Transposable element regulation and expression in cancer // FEBS J. 2022 V. 289. P. 1160–1179. doi: 10.1111/febs.15722
  31. Schwarz R., Koch P., Wilbrandt J., Hoffmann S. Locus-specific expression analysis of transposable elements // Brief Bioinform. 2022. V. 23. doi: 10.1093/bib/bbab417

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2. Fig. 1. Phylogenetic diversity of TLEWI transposons in the Pacific oyster. Bootstrap values ​​less than 50% are not shown in the dendrogram. The analysis used 38 amino acid sequences, the alignment length is 493 aa.

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3. Fig. 2. Transcriptional activity of the TLEWI transposase gene of the Pacific oyster during the development of the organism from egg to juvenile oyster.

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4. Fig. 3. Transcriptional activity of the TLEWI transposase gene in the gills of the Pacific oyster after the mollusks were exposed to different temperature conditions for seven days.

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5. Fig. 4. Transcriptional activity of the TLEWI transposase gene in Pacific oyster gills after 12-hour exposure of mollusks to different salinities.

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6. Fig. 5. Transcriptional activity of the TLEWI element transposase gene in the gills and muscles of the Pacific oyster during prolonged periods without water and food.

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7. Appendix 1
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