Peptidyl Transferase Center and the Emergence of the Translation System
Abstract
:1. Introduction
2. Materials and Methods
3. Results and Discussion
4. The Operational Code Revisited
5. Conclusions
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
- Petrov, A.S.; Williams, L.D. The ancient heart of the ribosomal large subunit: a response to Caetano-Anolles. J. Mol. Evol. 2015, 80, 166–170. [Google Scholar] [CrossRef] [PubMed]
- Petrov, A.S.; Gulen, B.; Norris, A.M.; Kovacs, N.A.; Bernier, C.R.; Lanier, K.A.; Fox, G.E.; Harvey, S.C.; Wartell, R.M.; Hud, N.V.; et al. History of the ribosome and the origin of translation. Proc. Natl. Acad. Sci. USA 2015, 15, 15396–15401. [Google Scholar] [CrossRef] [PubMed]
- Krupkin, M.; Matzov, D.; Tang, H.; Metz, M.; Kalaora, R.; Belousoff, M.J.; Zimmerman, E.; Bashan, A.; Yonath, A. A vestige of a prebiotic bonding machine is functioning within the contemporary ribosome. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 2001, 27, 2972–2978. [Google Scholar] [CrossRef] [PubMed]
- Davidovich, C.; Belousoff, M.; Bashan, A.; Yonath, A. The evolving ribosome: From non-coded peptide bond formation to sophisticated translation machinery. Res. Microbiol. 2009, 160, 487–492. [Google Scholar] [CrossRef] [PubMed]
- Fox, G.E. Origin and evolution of the ribosome. Cold Spring Harb. Perspect. Biol. 2010, 2, a003483. [Google Scholar] [CrossRef] [PubMed]
- Huang, L.; Krupkin, M.; Bashan, A.; Yonath, A.; Massa, L. Protoribosome by quantum kernel energy method. Proc. Natl. Acad. Sci. USA 2013, 10, 14900–14905. [Google Scholar] [CrossRef] [PubMed]
- Petrov, A.S.; Bernier, C.R.; Hsiao, C.; Norris, A.M.; Kovacs, N.A.; Waterbury, C.C.; Stepanov, V.G.; Harvey, S.C.; Fox, G.E.; Wartell, R.M.; et al. Evolution of the ribosome at atomic resolution. Proc. Natl. Acad. Sci. USA 2014, 111, 10251–10256. [Google Scholar] [CrossRef] [PubMed]
- Farias, S.T.; Rêgo, T.G.; José, M.V. Origin and evolution of the Peptidyl Transferase Center from proto-tRNAs. FEBS Openbio 2014, 8, 175–178. [Google Scholar] [CrossRef] [PubMed]
- Agmon, I.; Bashan, A.; Yonath, A. On ribosome conservation and evolution. Isr. J. Ecol. Evol. 2006, 52, 359–374. [Google Scholar] [CrossRef]
- Belousoff, M.J.; Davidovich, C.; Bashan, A.; Yonath, A. On the development towards the modern world: A plausible role of uncoded peptides in the RNA world. In Origins of Life and Evolution of Biospheres; Ruiz-Mirazo, K., Luisi, P.L., Eds.; Springer: New York City, NY, USA, 2010; pp. 415–419. [Google Scholar]
- Agmon, I.; Bashan, A.; Zarivach, R.; Yonath, A. Symmetry at the active site of the ribosome: Structural and functional implications. Biol. Chem. 2005, 386, 833–844. [Google Scholar] [CrossRef] [PubMed]
- Agmon, I. The dimeric proto-ribosome: Structural details and possible implications on the origin of life. Int. J. Mol. Sci. 2009, 30, 2921–2934. [Google Scholar] [CrossRef] [PubMed]
- Bashan, A.; Belousoff, M.J.; Davidovich, C.; Yonath, A. Linking the RNA world to modern life: The proto-ribosome conception. Orig. Life Evol. Biosph. 2010, 40, 425–429. [Google Scholar]
- Tamura, K. Ribosome evolution: Emergence of peptide synthesis machinery. J. Biosci. 2011, 36, 921–928. [Google Scholar] [CrossRef] [PubMed]
- Bloch, D.; McArthur, B.; Widdowson, R.; Spector, D.; Guimaraes, R.C.; Smith, J. tRNA-rRNA sequence homologies: a model for the origin of a common ancestral molecule, and prospects for its reconstruction. Orig. Life 1984, 14, 571–578. [Google Scholar] [CrossRef] [PubMed]
- Bloch, D.P.; McArthur, B.; Guimarães, R.C.; Smith, J.; Staves, M.P. tRNA-rRNA sequence matches from inter- and intraspecies comparisons suggest common origins for the two RNAs. Braz. J. Med. Biol. Res. 1989, 22, 931–944. [Google Scholar] [PubMed]
- Root-Bernstein, M.; Root-Bernstein, R. The ribosome as a missing link in the evolution of life. J. Theor. Biol. 2015, 21, 130–158. [Google Scholar] [CrossRef] [PubMed]
- Feng, S.; Chen, Y.; Kamada, K.; Wang, H.; Tang, K.; Wang, M.; Gao, Y.G. YoeB-ribosome structure: A canonical RNase that requires the ribosome for its specific activity. Nucleic Acids Res. 2013, 41, 9549–9556. [Google Scholar] [CrossRef] [PubMed]
- Rother, M.; Milanowska, K.; Puton, T.; Jeleniewicz, J.; Rother, K.; Bujnicki, J.M. ModeRNA server: An online tool for modeling RNA 3D structures. Bioinformatics 2011, 1, 2441–2442. [Google Scholar] [CrossRef] [PubMed]
- Cech, P.; Svozil, D.; Hoksza, D. SETTER: Web server for RNA structure comparison. Nucleic Acids Res. 2012, 40. [Google Scholar] [CrossRef] [PubMed]
- Ritchie, D.W.; Venkatraman, V. Ultra-fast FFT protein docking on graphics processors. Bioinformatics 2010, 1, 2398–2405. [Google Scholar] [CrossRef] [PubMed]
- Park, S.J.; Schimmel, P. Evidence for interaction of an aminoacyl transfer RNA synthetase with a region important for the identity of its cognate transfer RNA. J. Biol. Chem. 1988, 15, 16527–16530. [Google Scholar]
- Hou, Y.M.; Schimmel, P. A simple structural feature is a major determinant of the identity of a transfer RNA. Nature 1988, 12, 140–145. [Google Scholar] [CrossRef] [PubMed]
- Schimmel, P.; Giegé, R.; Moras, D.; Yokoyama, S. An operational RNA code for amino acids and possible relationship to genetic code. Proc. Natl. Acad. Sci. USA 1993, 1, 8763–8768. [Google Scholar] [CrossRef]
- Ribas de Pouplana, L.; Turner, R.J.; Steer, B.A.; Schimmel, P. Genetic code origins: tRNAs older than their synthetases? Proc. Natl. Acad. Sci. USA 1998, 15, 11295–11300. [Google Scholar] [CrossRef]
- Caetano-Anollés, G.; Wang, M.; Caetano-Anollés, D. Structural phylogenomics retrodicts the origin of the genetic code and uncovers the evolutionary impact of protein flexibility. PLoS ONE 2013, 21, e72225. [Google Scholar] [CrossRef] [PubMed]
- Shimizu, M. Specific aminoacylation of C4N hairpin RNAs with the cognate aminoacyl-adenylates in the presence of a dipeptide: origin of the genetic code. J. Biochem. 1995, 117, 23–26. [Google Scholar] [CrossRef] [PubMed]
- Farias, S.T.; Rêgo, T.G.; José, M.V. Evolution of transfer RNA and the origin of the translation system. Front. Genet. 2014, 28, 303. [Google Scholar] [CrossRef] [PubMed]
© 2017 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
Share and Cite
Torres de Farias, S.; Gaudêncio Rêgo, T.; José, M.V. Peptidyl Transferase Center and the Emergence of the Translation System. Life 2017, 7, 21. https://doi.org/10.3390/life7020021
Torres de Farias S, Gaudêncio Rêgo T, José MV. Peptidyl Transferase Center and the Emergence of the Translation System. Life. 2017; 7(2):21. https://doi.org/10.3390/life7020021
Chicago/Turabian StyleTorres de Farias, Savio, Thais Gaudêncio Rêgo, and Marco V. José. 2017. "Peptidyl Transferase Center and the Emergence of the Translation System" Life 7, no. 2: 21. https://doi.org/10.3390/life7020021
APA StyleTorres de Farias, S., Gaudêncio Rêgo, T., & José, M. V. (2017). Peptidyl Transferase Center and the Emergence of the Translation System. Life, 7(2), 21. https://doi.org/10.3390/life7020021