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The problem of the ‘prebiotic and never born proteins’

Published online by Cambridge University Press:  30 October 2012

Gerald E. Marsh*
Affiliation:
Argonne National Laboratory (Ret) 5433 East View Park, Chicago, IL 60615, USA e-mail: gemarsh@uchicago.edu

Abstract

It has been argued that the limited set of proteins used by life as we know could not have arisen by the process of Darwinian selection from all possible proteins. This probabilistic argument has a number of implicit assumptions that may not be warranted. A variety of considerations are presented to show that the number of amino acid sequences that need to have been sampled during the evolution of proteins is far smaller than assumed by the argument.

Type
Research Article
Copyright
Copyright © Cambridge University Press 2012

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References

Berg, J.M., Tymoczko, J.L. & Stryer, L. (2002). Biochemistry, 5th edn. W.H. Freeman and Co., New York, section 9.2.Google Scholar
Chiarabelli, C. & De Lucrezia, D. (2007). Question 3: the worlds of the prebiotic and never born proteins. Orig. Life Evol. Bioph. 37, 357361. See also the posts by ‘Retread’ at http://blogs.nature.com/thescepticalchymist/2008/04/chemiotics_how_many_proteins_c.htmlGoogle Scholar
Dyson, F. (1985). Origins of Life. Cambridge University Press, Cambridge.Google Scholar
Galperin, M.Y., Walker, D.R. & Koonin, E.V. (1998). Analogous enzymes: independent inventions in enzyme evolution. Genome Res. 8, 779790.CrossRefGoogle ScholarPubMed
Gherardini, P.F., Wass, M.N., Helmer-Citterich, M. & Sternberg, M.J.E. (2007). Convergent evolution of enzyme active sites is not a rare phenomenon. J. Mol. Biol. 372, 817845.Google Scholar
Harish, A. & Caetano-Anollés, G. (2012). Ribosomal history reveals origins of modern protein synthesis. PLoS ONE 7(3), e32776.Google Scholar
Hong, X., Murakami, H., Suga, H. & Ferré-D'Amaré, A.R. (2008). Structural basis of specific tRNA amonoacylation by a small in vitro selected ribozyme. Nature 457, 358361.Google Scholar
Illangasekare, M., Sanchez, G., Nickles, T. & Yarus, M. (1995). Aminoacyl-RNA synthesis catalyzed by an RNA. Science 267, 643647.Google Scholar
Kumar, R.K. & Yarus, M. (2001). RNA-catalyzed amino acid activation. Biochemistry 40, 69987004.CrossRefGoogle ScholarPubMed
Lazcano, A., Guerrero, R., Margulis, L. & Oró, J. (1988). The evolutionary transition from RNA to DNA in early cells. J. Mol. Evol. 27, 283290.Google Scholar
Leman, L., Orgel, L. & Reza Ghadiri, M. (2004). Carbonyl sulfide-mediated prebiotic formation of peptides. Science 306, 283286.Google Scholar
Levinthal, C. (1969). Mossbauer spectroscopy in biological systems. In Proceedings of a Meeting held at Allerton House, ed. Monticello, I.L., Debrunner, P., Tsibris, J.C.M. & Munck, E., pp. 2224. University of Illinois Press, Urbana, IL.Google Scholar
Llewellyn, N.M. & Spencer, J.B. (2007). Enzymes line up for assembly. Nature 448, 755756.Google Scholar
Miller, S.L. (1953). A production of amino acids under possible primitive earth conditions. Science 117, 528529. A recent reanalysis of the residues of one of the original Miller experiments using modern techniques [Johnson AP et al. (2008) The Miller Volcanic Spark Discharge Experiment. Science 322:404] showed the presence of 22 amino acids and five amines rather than the five amino acids originally found by Miller.Google Scholar
Miller, S.L. & Orgel, L.E. (1974). The Origins of Life on the Earth. Prentice-Hall Inc., Englewood Cliffs, NJ.Google Scholar
Morange, M. (2008). Fifty years of the Central Dogma. J. Biosci. 33(2), 171175.Google Scholar
Oparin, A.I. (1966). Life: Its Nature, Origin, and Development. Academic Press Inc., New York [Translated from the Russian by Ann Synge].Google Scholar
Orgel, L.E. (2004). Prebiotic chemistry and the origin of the RNA world. Crit. Rev. Biochem. Mol. Biol. 39, 99123.Google ScholarPubMed
Seiwert, S.D. (1996). RNA editing hints of a remarkable diversity in gene expression pathways. Science 274, 16361637.Google Scholar
Thieffry, D. & Sarkar, S. (1998). Forty years under the central dogma. Trends Biochem. Sci. 23, 312316.Google Scholar
van der Gulik, P., Massar, S., Gilis, D., Buhrman, H. & Rooman, M. (2009). The first peptides: the evolutionary transition between prebiotic amino acids and early proteins. J. Theor. Biol. 261, 531539.Google Scholar
Wei, Y., Kim, S., Fela, D., Baum, J. & Hecht, M.H. (2003). Solution structure of a de novo protein from a designed combinatorial library. Proc. Natl. Acad. Sci. U.S.A. 100, 1327013273.Google Scholar
Wong, J. (2005). Coevolution theory of the genetic code at age thirty. BioEssays 27, 416425.Google Scholar
Zhang, B., & Cech, T.R. (1998). Peptidyl-transferase ribozymes: trans reactions, structural characterization and ribosomal RNA-like features. Chem. Biol. 5, 539553.Google Scholar
Zwanzig, R., Szabo, A. & Bagchi, B. (1992). Levinthal's paradox. Proc. Natl. Acad. Sci. U.S.A. 89, 2022.Google Scholar