REVIEW ARTICLE Front. Genet., 20 May 2014 | doi: 10.3389/fgene.2014.00140
Redundancy of the genetic code enables translational pausing
David J. D'Onofrio 1,2 and David L. Abel 3
1Control Systems Modeling and Simulation, General Dynamics, Sterling Heights, MI, USA
2Department of Humanities and Science, Math Department, College of Humanities and Science, University of Phoenix, Detroit, MI, USA
3Department of ProtoBioCybernetics/ProtoBioSemiotics, The Gene Emergence Project of The Origin of Life Science Foundation, Inc., Greenbelt, MD, USA
The codon redundancy (“degeneracy”) found in protein-coding regions of mRNA also prescribes Translational Pausing (TP). When coupled with the appropriate interpreters, multiple meanings and functions are programmed into the same sequence of configurable switch-settings. This additional layer of Ontological Prescriptive Information (PIo) purposely slows or speeds up the translation-decoding process within the ribosome. Variable translation rates help prescribe functional folding of the nascent protein. Redundancy of the codon to amino acid mapping, therefore, is anything but superfluous or degenerate. Redundancy programming allows for simultaneous dual prescriptions of TP and amino acid assignments without cross-talk. This allows both functions to be coincident and realizable. We will demonstrate that the TP schema is a bona fide rule-based code, conforming to logical code-like properties. Second, we will demonstrate that this TP code is programmed into the supposedly degenerate redundancy of the codon table. We will show that algorithmic processes play a dominant role in the realization of this multi-dimensional code.
Keywords: algorithm, translational pausing, ribosome, regulation, co-translational folding, Shine Dalgarno sequences, degeneracy, multi-dimensional code
Citation: D'Onofrio DJ and Abel DL (2014) Redundancy of the genetic code enables translational pausing. Front. Genet. 5:140. doi: 10.3389/fgene.2014.00140
Received: 02 March 2014; Paper pending published: 27 March 2014;
Accepted: 28 April 2014; Published online: 20 May 2014.
Edited by:Firas H. Kobeissy, University of Florida, USA
Reviewed by:Firas H. Kobeissy, University of Florida, USA
Georges Nemer, American University of Beirut, Lebanon
Copyright © 2014 D'Onofrio and Abel. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: David J. D'Onofrio, Department of Humanities and Science, University of Phoenix, 4400 Town Center, Southfield, MI 48127, USA e-mail: email@example.com
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