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Volume 10   Issue 1   Year 2015
Skoblikow N.E., Zimin ΐ.ΐ.

A search for relict ribonucleotide and amino acid sequences that played a key role in the development of the ribosome and modern protein diversity

Mathematical Biology & Bioinformatics. 2015;10(1):116-130.

doi: 10.17537/2015.10.116.

References

  1. Koonin E.V. The Logic of Chance: The Nature and Origin of Biological Evolution. Upper Saddle River: FT Press; 2011. 528 p.
  2. Caetano-Anolles G., Wang M., Caetano-Anolles D., Mittenthal J.E. The origin, evolution and structure of the protein world. Biochem. J. 2009;417:621-637. doi: 10.1042/BJ20082063
  3. Sobolevsky Y., Guimarães R.C., Trifonov E.N. Towards functional repertoire of the earliest proteins. J. Biomol. Struct. Dyn. 2013;31(11):293-300. doi: 10.1080/07391102.2012.735623
  4. de Farias S.T., do Rêgo T.G., José M.V. Evolution of transfer RNA and the origin of the translation system. Front. Genet. 2014;5:03.
  5. Root-Bernstein M., Root-Bernstein R. The ribosome as a missing link in the evolution of life. Journal of Theoretical Biology. 2015;367(21):130-158. doi: 10.1016/j.jtbi.2014.11.025
  6. Greber B.J., Boehringer D., Leitner A., Bieri P., Voigts-Hoffmann F., Erzberger J.P., Leibundgut M., Aebersold R., Ban N. Reductive evolution of the mitochondrial 16S rRNA. Nature. 2014;505:515-519. doi: 10.1038/nature12890
  7. Bokov K., Steinberg S.V. A hierarchical model for evolution of 23S ribosomal RNA. Nature. 2009;457:977-980. doi: 10.1038/nature07749
  8. Hsiao Ch., Mohan S., Kalahar B.K., Williams L.D. Peeling the onion: ribosomes are ancient molecular fossils. Mol. Biol. Evol. 2009;26(11):2415-25. doi: 10.1093/molbev/msp163
  9. Polacek N., Mankin AS. The ribosomal peptidyl transferase center: structure, function, evolution, inhibition. Crit. Rev. Biochem. Mol. Biol. 2005;40(5):285-311. doi: 10.1080/10409230500326334
  10. Cavalier-Smith T. Rooting the tree of life by transition analyses. Biology Direct. 2006;1:19. doi: 10.1186/1745-6150-1-19
  11. Copley S.D., Smith E., Morowitz H.J. A mechanism for the association of amino acids with their codons and the origin of the genetic code. Proc Natl Acad Sci USA. 2005;102(12):4442-4447. doi: 10.1073/pnas.0501049102
  12. Miller S.L., Urey H.C. Organic compound synthesis on the primitive Earth. Science. 1959;3370(130):45-251.
  13. GENBANK Entrez Nucleotide Database. http://www.ncbi.nlm.nih.gov/nucleotide/ (accessed 15.03.2015).
  14. Basic Local Alighnment Search Tool. http://blast.ncbi.nlm.nih.gov/Blast.cgi (accessed. 15.03.2015).
  15. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J. Mol. Biol. 1990;215(3):403-410. doi: 10.1016/S0022-2836(05)80360-2
  16. Jeanmougin F., Thompson J.D., Gouy M., Higgins D.G., Gibson T.J. Multiple sequence alignment with Clustal X. Trends Biochem. Sci. 1998;23:403-405. doi: 10.1016/S0968-0004(98)01285-7
  17. Woese C. The universal ancestor. PNAS. 1998;95(12):6854-6859. doi: 10.1073/pnas.95.12.6854
  18. Petrov A.S., Bernier C.R., Hsiao Ch., Norris A.M., Kovacs N.A., Waterbury C.C., Stepanov V.G., Harvey S.C., Fox G.E., Wartell R.M., Hud N.V., Williams L.D. Evolution of the ribosome at atomic resolution. PNAS. 2014;111(28):10251-10256. doi: 10.1073/pnas.1407205111
  19. Tamura K. Ribosome evolution: Emergence of peptide synthesis machinery. Journal of Biosciences. 2011;36(5):921-928. doi: 10.1007/s12038-011-9158-2
  20. Harish A., Caetano-Anollés G. Ribosomal History Reveals Origins of Modern Protein Synthesis. PLoS One. 2012;7(3):e32776. doi: 10.1371/journal.pone.0032776
  21. Pascal R. Boiteau L., Forterre P., Gargaud M., Lazcano A., Lopez-Garcia P., Maurel M-C., Moreira D., Pereto J., Prieur D., Reisse J. Prebiotic Chemistry - Biochemistry Emergence of Life (4.4 2 Ga). Earth, Moon and Planets. 2007;98:153-203. doi: 10.1007/s11038-006-9089-3
  22. Mulkidjanian A.Y., Galperin M.Y. On the origin of life in the zinc world. 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth. Biol. Direct. 2009;4:27. doi: 10.1186/1745-6150-4-27
  23. Saladino R., Botta G., Pino S., Costanzo G., Di Mauro E. Genetics first or metabolism first? The formamide clue. Chem. Soc. Rev. 2012;41(16):5526-5565. doi: 10.1039/c2cs35066a
  24. Pino S., Sponer J.E., Costanzo G., Saladino R., Di Mauro E. From Formamide to RNA, the Path Is Tenuous but Continuous. Life. 2015;5:372-384. doi: 10.3390/life5010372
  25. Müller U.F., Bartel D.P. Improved polymerase ribozyme efficiency on hydrophobic assemblies. RNA. 2008;14(3):552-562. doi: 10.1261/rna.494508
Table of Contents
Original Article
Math. Biol. Bioinf.
2015;10(1):116-130
doi: 10.17537/2015.10.116
published in English

Abstract (eng.)
Abstract (rus.)
Full text (eng., pdf)
References
Translation into Russian
Math. Biol. Bioinf.
2015;10(1):t39-t55
doi: 10.17537/2015.10.t39

Full text (rus., pdf)

 
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