| Peer-Reviewed

An Analysis of Cumulative Selection and Random Drift in the Evolutionary Origination of Novel Protein Motifs

Received: 6 August 2013     Published: 30 August 2013
Views:       Downloads:
Abstract

Despite the fact that all-important protein motifs encoded in gene sequences are generally considered to have been generated solely through a gradual and undirected process of change, the idea lacks empirical evidence and also suffers from theoretical difficulties. More recently, sudden developments such as through the exonization of non-coding DNA, as well as frameshift mutation, have been suggested as another source of evolutionary innovation. A mathematical model was used here to describe the combined action of both cumulative natural selection and random drift, relative to that of an alternative mechanism of artificial selection, in the origination of a hypothetical multi-residue sequence motif. A computer simulation of the model quantifiably demonstrates the marked inefficacy of standard forces in developing these molecular features when compared to the power of a directed or self-organizing process. An examination of how natural population shifts, including migration and isolation, as well as intragenic recombination, may serve to facilitate this particular case is also explored. An evolutionary accretion for novel motifs is concluded as being eminently feasible, although not one wholly reliant on the outcome of chance and differential reproduction.

Published in Computational Biology and Bioinformatics (Volume 1, Issue 4)
DOI 10.11648/j.cbb.20130104.11
Page(s) 15-21
Creative Commons

This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.

Copyright

Copyright © The Author(s), 2013. Published by Science Publishing Group

Keywords

Cumulative Selection, Protein Motifs, Functional Adaptation, Directed Evolution

References
[1] Kanapin, A.A, Mulder N, Kuznetsov V.A. [2010]. Projection of gene-protein networks to the functional space of the proteome and its application to analysis of organism complexity.BMC Genomics.;11 Suppl 1:S4.
[2] Malek, J.A. [2001]. Abundant protein domains occur in proportion to proteome size. Genome Biology. doi:10.1186/gb-2001-2-9-research0039
[3] Ewens, W.J, Wilf, H.S. [2010]. There’s plenty of time for evolution. Proceedings of the National Academy of Sciences, Vol. 107, No. 52. pp. 22454-22456. doi:10.1073/pnas.1016207107
[4] Salthe, S.N.[2008]. Natural selection in relation to complexity. Artif Life.;14(3):363-74.
[5] Scherer, S.W, Feuk, L, Marquès-Bonet, T, Navarro, A, Okamura, K. [2006]. Frequent appearance of novel protein-coding sequences by frameshift translation. Genomics; 88:690–697
[6] Knowles, D., McLysaght, A [2009]. A. Recent de novo origin of human protein-coding genes. Genome research, 2009; Vol. 19, No. 10, pp. 1752-1759.
[7] Gregory, T. [2009]. Artificial Selection and Domestication: Modern Lessons from Darwin’s Enduring Analogy. Evolution: Education and Outreach. Volume 2, Number 1, 5-27, DOI: 10.1007/s12052-008-0114-z
[8] Dougherty, M.J, Arnold, F.H. [2009]. Directed evolution: new parts and optimized function. Curr Opin Biotechnol.;20(4):486-91.
[9] Lynch, M., Abegg, A. [2010]. The rate of establishment of complex adaptations Mol Biol Evol.;27(6):1404-14.
[10] Jäckel C, Kast P, Hilvert D. [2008] .Protein design by directed evolution.Annu Rev Biophys. ;37:153-73.
[11] Romero, P.A., Arnold F.H., [2009]. Exploring protein fitness landscapes by directed evolution. Nat Rev Mol Cell Biol.;10(12):866-76.
[12] Gillespie, J.H.[1991]. The Causes of Molecular Evolution. Oxford University Press, New York.
[13] Ohta T .[1993].Interaction of selection and drift in molecular evolution. Jpn. J. Genet. 68, pp. 529-537
[14] Lynch, M. [2010]. Scaling expectations for the time to establishment of complex adaptations.Proc Natl Acad Sci U S A.;107(38):16577-82.
[15] Ohno, S. [1970]. Evolution by Gene Duplication (Springer, Heidelberg).
[16] Zhang J.[2003]. Evolution by gene duplication: an update. Trends in Ecology & Evolution 18 (6): 292-298. doi:10.1016/S0169-5347(03)00033-8 To insert individual citation into a bibliography in a word-processor, select your preferred citation style below and drag-and-drop it into the document.
[17] Johnson, A.D. ,[2009]. Single-nucleotide polymorphism bioinformatics: a comprehensive review of resources. Circ Cardiovasc Genet.;2(5):530-6.
[18] Balin SJ, Cascalho M.[2010]. The rate of mutation of a single gene. Nucleic Acids Res.;38(5):1575-82. doi: 10.1093/nar/gkp1119.
[19] Yang, Z., Yoder A., [1999]. Estimation of the transition/transversion rate bias and species sampling. J. Mol. Evol. 48, pp. 274–283
[20] Cusumano, A. (1998). The harmonic series diverges. American Mathematical Monthly 105(7), 608.
[21] Melzer, N., Villmann, C., Becker, K., Harvey, K., Harvey, R.J., Vogel, N., Kluck, C.J., Kneussel M., Becker CM. [2010]. Multifunctional basic motif in the glycine receptor intracellular domain induces subunit-specific sorting. J Biol Chem.;285(6):3730-9.
[22] Rorick M.M, Wagner G.P. [2010]. The origin of conserved protein domains and amino acid repeats via adaptive competition for control over amino acid residues. J Mol Evol.;70(1):29-43.
[23] Ledneva, R.K., Alexeevskii, A.V., Vasil, S.A., Spirin, S.A., Karyagina A.S.[2001]. Structural aspects of interaction of homeodomains withDNA. Mol Biol 35(5):647–659
[24] Thorell S, Gergely P, Banki K, Perl A, Schneider G [2000]. "The three-dimensional structure of human transaldolase". FEBS Lett. 475 (3): 205–8.
[25] Gokhale, C.S, Iwasa, Y., Nowak, M.A, Traulsen, A. [2000]. The pace of evolution across fitness valleys J Theor Biol. 2009 7;259(3):613-20.
[26] McPherson, G. [1990]. Statistics in scientific investigation: its basis, application and interpretation. Springer-Verlag
[27] Gromiha, M.M, Selvaraj, S (2004). Inter-residue Interactions in Protein Folding and Stability. Prog. Biophys. Mol. Biol. 86, 235-277.
[28] Viguera E, Canceill D, Ehrlich S.D.[2001]. Replication slippage involves DNA polymerase pausing and dissociation. EMBO J.;20(10):2587-95.
[29] Kimura, M.,[1962]. On the probability of fixation of mutant genes in a population. Genetics. 47(6): 713–719.
[30] Ohta T. [1972].Population size and rate of evolution. J Mol Evol.;1(3):305-14.
[31] Frankham, R.(1996). Relationship of genetic variation to population size. Conservation biology pages 1500-1508; volume 10, no. 6.
[32] Arnold,F.H., Georgiou,G. [2003]. Directed Enzyme Evolution: Screening and Selection Methods. Humana Press, Clifton, NJ.
[33] Lande, R. [1980]. "Genetic Variation and Phenotypic Evolution During Alliopatric Speciation". The American Naturalist 116: 463-479. http://www.jstor.org/pss/2460440.
[34] Stadler, D.R, [1973]. The Mechanism of Intragenic Recombination. Annual Review of Genetics. Vol. 7: 113-127 doi: 10.1146/annurev.ge.07.120173.000553
[35] Batten, D., Salthe, S., Boschetti, F. [2009].Visions of Evolution: self-organization proposes what natural selection disposes. Biological Theory 3 (1):17-29.
[36] Lang, G.I., Murray, A.W.[2008]. Estimating the per-base-pair mutation rate in the yeast Saccharomyces cerevisiae.Genetics. ;178(1):67-82.
Cite This Article
  • APA Style

    Joseph E. Hannon Bozorgmehr. (2013). An Analysis of Cumulative Selection and Random Drift in the Evolutionary Origination of Novel Protein Motifs. Computational Biology and Bioinformatics, 1(4), 15-21. https://doi.org/10.11648/j.cbb.20130104.11

    Copy | Download

    ACS Style

    Joseph E. Hannon Bozorgmehr. An Analysis of Cumulative Selection and Random Drift in the Evolutionary Origination of Novel Protein Motifs. Comput. Biol. Bioinform. 2013, 1(4), 15-21. doi: 10.11648/j.cbb.20130104.11

    Copy | Download

    AMA Style

    Joseph E. Hannon Bozorgmehr. An Analysis of Cumulative Selection and Random Drift in the Evolutionary Origination of Novel Protein Motifs. Comput Biol Bioinform. 2013;1(4):15-21. doi: 10.11648/j.cbb.20130104.11

    Copy | Download

  • @article{10.11648/j.cbb.20130104.11,
      author = {Joseph E. Hannon Bozorgmehr},
      title = {An Analysis of Cumulative Selection and Random Drift in the Evolutionary Origination of Novel Protein Motifs},
      journal = {Computational Biology and Bioinformatics},
      volume = {1},
      number = {4},
      pages = {15-21},
      doi = {10.11648/j.cbb.20130104.11},
      url = {https://doi.org/10.11648/j.cbb.20130104.11},
      eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.cbb.20130104.11},
      abstract = {Despite the fact that all-important protein motifs encoded in gene sequences are generally considered to have been generated solely through a gradual and undirected process of change, the idea lacks empirical evidence and also suffers from theoretical difficulties. More recently, sudden developments such as through the exonization of non-coding DNA, as well as frameshift mutation, have been suggested as another source of evolutionary innovation. A mathematical model was used here to describe the combined action of both cumulative natural selection and random drift, relative to that of an alternative mechanism of artificial selection, in the origination of a hypothetical multi-residue sequence motif. A computer simulation of the model quantifiably demonstrates the marked inefficacy of standard forces in developing these molecular features when compared to the power of a directed or self-organizing process. An examination of how natural population shifts, including migration and isolation, as well as intragenic recombination, may serve to facilitate this particular case is also explored. An evolutionary accretion for novel motifs is concluded as being eminently feasible, although not one wholly reliant on the outcome of chance and differential reproduction.},
     year = {2013}
    }
    

    Copy | Download

  • TY  - JOUR
    T1  - An Analysis of Cumulative Selection and Random Drift in the Evolutionary Origination of Novel Protein Motifs
    AU  - Joseph E. Hannon Bozorgmehr
    Y1  - 2013/08/30
    PY  - 2013
    N1  - https://doi.org/10.11648/j.cbb.20130104.11
    DO  - 10.11648/j.cbb.20130104.11
    T2  - Computational Biology and Bioinformatics
    JF  - Computational Biology and Bioinformatics
    JO  - Computational Biology and Bioinformatics
    SP  - 15
    EP  - 21
    PB  - Science Publishing Group
    SN  - 2330-8281
    UR  - https://doi.org/10.11648/j.cbb.20130104.11
    AB  - Despite the fact that all-important protein motifs encoded in gene sequences are generally considered to have been generated solely through a gradual and undirected process of change, the idea lacks empirical evidence and also suffers from theoretical difficulties. More recently, sudden developments such as through the exonization of non-coding DNA, as well as frameshift mutation, have been suggested as another source of evolutionary innovation. A mathematical model was used here to describe the combined action of both cumulative natural selection and random drift, relative to that of an alternative mechanism of artificial selection, in the origination of a hypothetical multi-residue sequence motif. A computer simulation of the model quantifiably demonstrates the marked inefficacy of standard forces in developing these molecular features when compared to the power of a directed or self-organizing process. An examination of how natural population shifts, including migration and isolation, as well as intragenic recombination, may serve to facilitate this particular case is also explored. An evolutionary accretion for novel motifs is concluded as being eminently feasible, although not one wholly reliant on the outcome of chance and differential reproduction.
    VL  - 1
    IS  - 4
    ER  - 

    Copy | Download

Author Information
  • School of Informatics, University of Manchester, Manchester M13 9PL, United Kingdom

  • Sections