The Unexpected Strategies behind Alternative Genetic Codes

Jef Struyf^1,

¹A Retired Lecturer of UCLL Campus Gasthuisberg, Chemistry Bachelors Herestraat 49, Be-3000 Leuven, Belgium

Cite this paper:
Jef Struyf. The Unexpected Strategies behind Alternative Genetic Codes. American Journal of Educational Research. 2021; 9(7):417-425. doi: 10.12691/education-9-7-4

Abstract

This article proposes a number of codon reassignment strategies. These strategies are inferred by comparing the alternative (non-standard) genetic codes to the standard genetic code. Codon reassignments show strong and non-random connection to the standard code. The strategies interconnect all genetic codes and model a selected pathway through the heterotrophic part of life. The article also shows that the codon reassignment strategies model the evolution from the standard to the vertebrate mitochondrial code. Furthermore, it introduces a genetic code table based on third position synonyms that compares the vertebrate mitochondrial code to the standard code.

Keywords:
alternative genetic codes biochemical strategies codon reassignments codon reassignment strategies codon reassignment tables genetic code table molecular evolution molecular genetics non-standard genetic codes table for alternative genetic codes table for non-standard genetic codes

This work is licensed under a Creative Commons Attribution 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

Figures

References:

[1]	Struyf, J., “Parallelism between the Classical Geocentric Cosmos and the Life Chemistry Essentials” American Journal of Educational Research, 9, (1), 38-51, January 2021.
[2]	Nirenberg, M.W., “Deciphering the Genetic Code – a Personal Account” (Historical Review). Trends in Biochemical Sciences 29 (1). 46-54, January 2004.
[3]	Elzanowski, A., Ostell, J., “The Genetic Codes” Last update: Jan. 7 2019. https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi.
[4]	https://www.bioinformatics.org/sms/iupac.html.
[5]	Wichmann, S., Ardern, Z., “Optimality with standard genetic code is robust with respect to comparison code sets” Biosystems 185, 11, 104023, 2019.
[6]	Bezerra, A., Guimarães, A., Santos, M., “Non-Standard Genetic Codes Define New Concepts for Protein Engineering” Life 5 (4), 1610-1628, 2015.
[7]	Sammet, S., Bastolla, U., Porto, M., “Comparison of translation loads for standard and alternative genetic codes” BMC Evol Biol 10, 178, 2010.
[8]	Sengupta, S., Higgs, P., 2005 “A unified model of codon reassignment in alternative genetic codes” Genetics 170 (2): 831-840, 2005.
[9]	Link, J. A., Tirrell, D. A., “Reassignment of sense codons in vivo” Methods, 36 (3), 291-298, 2005.
[10]	Ring, K.L., Cavalcanti, A.R.O., Consequences of Stop Codon Reassignment on Protein Evolution in Ciliates with Alternative Genetic Codes, Mol. Biol. and Evol., 25, (1), 179-186, 2008.
[11]	Silva, R.M., Miranda, I., Moura, G., Santos, M.A.S., Yeast as a model organism for studying the evolution of nonstandard genetic codes, Henry Stewart Publications 1473-9550. Briefings In Functional Genomics And Proteomics, 3 (1), 35-46, April 2004.
[12]	Tuite, M.F., Santos, M.A.S., Codon reassignment in Candida species: An evolutionary conundrum, Biochimie 78, 993-999, 1996.
[13]	Osawa, S., Jukes, T.H., Codon reassignment (codon capture) in evolution, J Mol Evol. 28 (4), 271-8, 1989.
[14]	Santos, M., Moura, G., Massey, S., Tuite, M., “Driving change: the evolution of alternative genetic codes” Trends Genet 20 (2): 95-102, 2004.
[15]	Osawa, S., Ohama, T., Jukes, T.H., Watanabe, K., Evolution of the mitochondrial genetic code. I. Origin of AGR serine and stop codons in metazoan mitochondria, J Mol Evol. 29 (3), 202-7, 1989.
[16]	Knight, ,R.D., Landweber, L.F., Yarus, M., How mitochondria redefine the code, J Mol Evol . 53 (4-5), 299-313, Oct-Nov 2001.
[17]	Andersson, S. G. E., Kurland, C. G., “An extreme codon preference strategy: codon reassignment”. Mol. Biol. Evol., 8 (4), 530-544, 1991.
[18]	Ma, N.J., Hemez, C.F., Barber, K.W., Rinehart, J., Isaacs, F.J., Organisms with alternative genetic codes resolve unassigned codons via mistranslation and ribosomal rescue, eLife. 7, 2018, https://elifesciences.org/articles/34878.
[19]	Sengupta, S., Xiaoguang Yang, X., Higgs, P.G., The Mechanisms of Codon Reassignments in Mitochondrial Genetic Codes, https://arxiv.org/ftp/q-bio/papers/0703/0703066.pdf.
[20]	Blazej, P., Wnętrzak, M., Mackiewicz, D., Gagat, P., Mackiewicz, P., Many alternative and theoretical genetic codes are more robust to amino acid replacements than the standard genetic code, J. of Theoretical Biology, 7, March 21-32, 2019.
[21]	Röttinger, E., and Lowe, C. J. “Evolutionary crossroads in developmental biology: hemichordates” Development 139: 2463-2475, 2012.
[22]	Lekomtsev, S. A., Nonstandard genetic codes and translation termination, Molecular Biology. 41, 878-885, 2007.
[23]	Shu, J., 2017 “A new integrated symmetrical table for genetic codes” BioSystems 151: 21-26. 2017.
[24]	Shcherbak, V., “The co-operative symmetry of the genetic-code” J. of Theoretical Biology 132 (1): 121-124, 1988.
[25]	Findley, G., Findley, A., McGlynn, S., “Symmetry characteristics of the genetic code” Proc Natl Acad Sci 79 (22) 7061-7065, 1982.
[26]	Struyf, J., “The Human Hands Model for the Essentials of the Chemistry of Life” World Journal of Chemical Education, 6 (3): 117-123, 2018.
[27]	Margulis, L., Origin of Eukaryotic Cells, Yale University Press, 1970.