On the fundamental nature and evolution of the genetic code
Abstract
The present symposium defines clearly the current state of our knowledge of the genetic code. On one level we possess a high degree of comprehension of the code. And continuation of the present lines of research (based for the most part upon certain in vitro systems plus complementing in vivo studies) promises soon to complete our understanding of the code on this level. We now know, for example, essentially all of the codon assignments; we are making significant strides in elucidating the genetic sequences concerned with punctuation and modulation and with the (possibly) related phenomenon of relative codon usage; and we are beginning to understand the complex mechanisms involved in gene transcription and translation.
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The RNA world theory posits that RNA fulfilled both catalysis and information storage during an early stage of life.
“The RNA world theory posits that RNA fulfilled both of the major cellular functions, catalysis and information storage, during an early stage of life (1–3).”
From The prebiotic evolutionary advantage of transferring genetic information from RNA to DNA (2011) · cites this paper as [1]
The biology of modern organisms is based on RNA, DNA and proteins, but this biochemistry was probably preceded by a stage in which RNA molecules acted both as chemical catalysts and carriers of genetic information.
“The biology of modern organisms is based on RNA, DNA and proteins, but this biochemistry was probably preceded by a stage in which RNA molecules acted both as chemical catalysts and carriers of genetic information.”
From Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences (2012) · cites this paper as [4]
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Adaptive Computation and Machine Learning
(2012) · The MIT Press eBooks · doi:10.7551/mitpress/8291.003.0026 · Cited by 1,453 · see citing works
Aminoacyl-tRNA Synthetases, the Genetic Code, and the Evolutionary Process
Woese, C. R., Olsen, G. J., Ibba, M., & Söll, D. (2000) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.64.1.202-236.2000 · Cited by 706 · see citing works
Self-citationThe genetic code is one in a million
Freeland, S. J., & Hurst, L. D. (1998) · Journal of Molecular Evolution · doi:10.1007/pl00006381 · Cited by 563 · see citing works
Recent Evidence for Evolution of the Genetic Code
Jukes, T. H., & Osawa, S. (1991) · Springer eBooks · doi:10.1007/978-4-431-68302-5_6 · Cited by 506 · see citing works
Knight, R. D., Freeland, S. J., & Landweber, L. F. (2001) · Genome biology · doi:10.1186/gb-2001-2-4-research0010 · Cited by 439 · see citing works
Origin and evolution of the genetic code: The universal enigma
Koonin, E. V., & Novozhilov, A. S. (2009) · IUBMB Life · doi:10.1002/iub.146 · Cited by 392 · see citing works
Collective evolution and the genetic code
Vetsigian, K., Woese, C., & Goldenfeld, N. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0603780103 · Cited by 379 · see citing works
Self-citationA quantitative measure of error minimization in the genetic code
Haig, D., & Hurst, L. D. (1991) · Journal of Molecular Evolution · doi:10.1007/bf02103132 · Cited by 337 · see citing works
Budiša, N. (2004) · Angewandte Chemie International Edition · doi:10.1002/anie.200300646 · Cited by 263 · see citing works
Wolf, Y. I., & Koonin, E. V. (2007) · Biology Direct · doi:10.1186/1745-6150-2-14 · Cited by 235 · see citing works
“The early attempts to establish specificity in interactions of (poly)amino acids and polynucleotides have been inconclusive, indicating that, if a correspondence exists, it must be much less than precise, and the interactions involved would be weak and dependent on extraneous factors [94-96].”
BackgroundEarly Fixation of an Optimal Genetic Code
Freeland, S. J., Knight, R. D., Landweber, L. F., & Hurst, L. D. (2000) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026331 · Cited by 241 · see citing works
The RNA world as a model system to study the origin of life
Pressman, A., Blanco, C., & Chen, I. A. (2015) · Current Biology · doi:10.1016/j.cub.2015.06.016 · Cited by 225 · see citing works
Coevolution theory of the genetic code at age thirty
Wong, J. T.-F. (2005) · BioEssays · doi:10.1002/bies.20208 · Cited by 218 · see citing works
Optimality of the genetic code with respect to protein stability and amino-acid frequencies
Gilis, D., Massar, S., Cerf, N. J., & Rooman, M. J. (2001) · Genome biology · doi:10.1186/gb-2001-2-11-research0049 · Cited by 216 · see citing works
A Specific Amino Acid Binding Site Composed of RNA
Yarus, M. (1988) · Science · doi:10.1126/science.3381099 · Cited by 202 · see citing works
THE GENETIC CODE AND ERROR TRANSMISSION
Alff-Steinberger, C. (1969) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.64.2.584 · Cited by 167 · see citing works
The Case for an Error Minimizing Standard Genetic Code
Freeland, S. J., Wu, T., & Keulmann, N. (2003) · Origins of Life and Evolution of Biospheres · doi:10.1023/a:1025771327614 · Cited by 170 · see citing works
Gilis, D., & Rooman, M. J. (2000) · Protein Engineering Design and Selection · doi:10.1093/protein/13.12.849 · Cited by 161 · see citing works
The genetic code as a periodic table
Jungck, J. R. (1978) · Journal of Molecular Evolution · doi:10.1007/bf01734482 · Cited by 161 · see citing works
The origin of the genetic code: Theories and their relationships, a review
Giulio, M. D. (2005) · Biosystems · doi:10.1016/j.biosystems.2004.11.005 · Cited by 157 · see citing works
Comprehensive experimental fitness landscape and evolutionary network for small RNA
Jiménez, J. I., Xulvi-Brunet, R., Campbell, G. W., Turk-MacLeod, R., & Chen, I. A. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1307604110 · Cited by 140 · see citing works
Cavalier‐Smith, T. (2001) · Journal of Molecular Evolution · doi:10.1007/s002390010245 · Cited by 156 · see citing works
Mcclellan, D. A., Palfreyman, E., Smith, M., Moss, J. L., Christensen, R., & Sailsbery, J. K. (2005) · Molecular biology and evolution · doi:10.1093/molbev/msi028 · Cited by 154 · see citing works
Higgs, P. G. (2009) · Biology Direct · doi:10.1186/1745-6150-4-16 · Cited by 137 · see citing works
Aminoacyl-tRNA synthetases: potential markers of genetic code development
de Pouplana, L. R., & SCHIMMEL, P. R. (2001) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(01)01932-6 · Cited by 154 · see citing works
Amino Acids as RNA Ligands: A Direct-RNA-Template Theory for the Code's Origin
Yarus, M. (1998) · Journal of Molecular Evolution · doi:10.1007/pl00006357 · Cited by 138 · see citing works
Woese, C. R. (1973) · The Science of Nature · doi:10.1007/bf00592854 · Cited by 141 · see citing works
Self-citationCoding coenzyme handles: a hypothesis for the origin of the genetic code.
Szathmáry, E. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.21.9916 · Cited by 135 · see citing works
What Amino Acid Properties Affect Protein Evolution?
Xia, X., & Li, W. (1998) · Journal of Molecular Evolution · doi:10.1007/pl00006412 · Cited by 125 · see citing works
Novozhilov, A. S., Wolf, Y. I., & Koonin, E. V. (2007) · Biology Direct · doi:10.1186/1745-6150-2-24 · Cited by 122 · see citing works
Giulio, M. D. (1989) · Journal of Molecular Evolution · doi:10.1007/bf02103616 · Cited by 122 · see citing works
McClellan, D. A., & McCracken, K. G. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003892 · Cited by 119 · see citing works
Barbieri, M. (2017) · Biosystems · doi:10.1016/j.biosystems.2017.10.005 · Cited by 117 · see citing works
Which effective property of amino acids is best preserved by the genetic code?
Trinquier, G., & Sanejouand, Y. (1998) · Protein Engineering Design and Selection · doi:10.1093/protein/11.3.153 · Cited by 112 · see citing works
Role of minimization of chemical distances between amino acids in the evolution of the genetic code.
Wong, J. T.-F. (1980) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.77.2.1083 · Cited by 98 · see citing works
Pressman, A., Liu, Z., Janzen, E., Blanco, C., Müller, U. F., Joyce, G. F., Pascal, R., & Chen, I. A. (2019) · Journal of the American Chemical Society · doi:10.1021/jacs.8b13298 · Cited by 97 · see citing works
Coevolution of genetic code and amino acid biosynthesis
Tze-Fei Wong, J. (1981) · Trends in Biochemical Sciences · doi:10.1016/0968-0004(81)90013-x · Cited by 95 · see citing works
Cascade of reduced speed and accuracy after errors in enzyme-free copying of nucleic acid sequences
Leu, K., Kervio, E., Obermayer, B., Turk-MacLeod, R. M., Yuan, C., Luevano, J.-M., Chen, E., Gerland, U., Richert, C., & Chen, I. A. (2013) · Journal of the American Chemical Society · doi:10.1021/ja3095558 · Cited by 78 · see citing works
News from the Protein Mutability Landscape
Hecht, M., Bromberg, Y., & Rost, B. (2013) · Journal of Molecular Biology · doi:10.1016/j.jmb.2013.07.028 · Cited by 88 · see citing works
The prebiotic evolutionary advantage of transferring genetic information from RNA to DNA
Leu, K., Obermayer, B., Rajamani, S., Gerland, U., & Chen, I. A. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr525 · Cited by 85 · see citing works
Nucleotide composition as a driving force in the evolution of retroviruses
Bronson, E. C., & Anderson, J. N. (1994) · Journal of Molecular Evolution · doi:10.1007/bf00178851 · Cited by 80 · see citing works
Budiša, N. (2004) · Angewandte Chemie · doi:10.1002/ange.200300646 · Cited by 77 · see citing works
The Coevolution of Genes and Genetic Codes: Crick’s Frozen Accident Revisited
Sella, G., & Ardell, D. H. (2006) · Journal of Molecular Evolution · doi:10.1007/s00239-004-0176-7 · Cited by 77 · see citing works
Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences
Derr, J., Manapat, M. L., Rajamani, S., Leu, K., Xulvi-Brunet, R., Joseph, I., Nowak, M. A., & Chen, I. A. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks065 · Cited by 74 · see citing works
Davis, B. K. (1999) · Progress in Biophysics and Molecular Biology · doi:10.1016/s0079-6107(99)00006-1 · Cited by 73 · see citing works
One Polypeptide with Two Aminoacyl-tRNA Synthetase Activities
Stathopoulos, C., Li, T., Longman, R., Vothknecht, U. C., Becker, H. D., Ibba, M., & Söll, D. G. (2000) · Science · doi:10.1126/science.287.5452.479 · Cited by 72 · see citing works
Giulio, M. D., & Medugno, M. (1999) · Journal of Molecular Evolution · doi:10.1007/pl00006522 · Cited by 70 · see citing works
Some aspects of the organization and evolution of the genetic code
Giulio, M. D. (1989) · Journal of Molecular Evolution · doi:10.1007/bf02100202 · Cited by 70 · see citing works
On the Evolution of Redundancy in Genetic Codes
Ardell, D. H., & Sella, G. (2001) · Journal of Molecular Evolution · doi:10.1007/s002390010217 · Cited by 68 · see citing works
YARUS, M., & CHRISTIAN, E. L. (1989) · Nature · doi:10.1038/342349b0 · Cited by 67 · see citing works
Evolution of the aminoacyl-tRNA synthetases and the origin of the genetic code
Wetzel, R. B. (1995) · Journal of Molecular Evolution · doi:10.1007/bf00166624 · Cited by 67 · see citing works
Isoleucine:RNA sites with associated coding sequences.
Majerfeld, I. H., & Yarus, M. (1998) · Europe PMC (PubMed Central) · Cited by 67 · see citing works
Participation of isomeric tRNA'S in the partial reactions of protein biosynthesis
Hecht, S. M. (1977) · Tetrahedron · doi:10.1016/0040-4020(77)84042-8 · Cited by 67 · see citing works
Load minimization of the genetic code: history does not explain the pattern
Freeland, S. J., & Hurst, L. D. (1998) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.1998.0547 · Cited by 59 · see citing works
No accident: genetic codes freeze in error–correcting patterns of the standard genetic code
Ardell, D. H., & Sella, G. (2002) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2002.1071 · Cited by 59 · see citing works
Further results on error minimization in the genetic code
Goldman, N. (1993) · Journal of Molecular Evolution · doi:10.1007/bf00182752 · Cited by 57 · see citing works
On the optimality of the genetic code, with the consideration of termination codons
Goodarzi, H., Nejad, H. A., & Torabi, N. (2004) · Biosystems · doi:10.1016/j.biosystems.2004.05.031 · Cited by 55 · see citing works
A harmonic structure of the genetic code
Rakočević, M. M. (2004) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2004.03.017 · Cited by 55 · see citing works
Protein map: An alignment-free sequence comparison method based on various properties of amino acids
Yu, C., Cheng, S.-Y., He, R. L., & Yau, S. S. ‐. (2011) · Gene · doi:10.1016/j.gene.2011.07.002 · Cited by 54 · see citing works
Tropsha, A., Kizer, J. S., & CHAIKEN, I. M. (1992) · Journal of Molecular Recognition · doi:10.1002/jmr.300050202 · Cited by 53 · see citing works
The evolution of the genetic code: Impasses and challenges
Kun, Á., & Radványi, Á. (2017) · Biosystems · doi:10.1016/j.biosystems.2017.10.006 · Cited by 52 · see citing works
Giulio, M. D. (2001) · Journal of Theoretical Biology · doi:10.1006/jtbi.2000.2206 · Cited by 53 · see citing works
Judson, O. P., & Haydon, D. T. (1999) · Journal of Molecular Evolution · doi:10.1007/pl00006575 · Cited by 52 · see citing works
Giulio, M. D., & Medugno, M. (1998) · Journal of Molecular Evolution · doi:10.1007/pl00006341 · Cited by 49 · see citing works
Błażej, P., Wnętrzak, M., Mackiewicz, D., & Mackiewicz, P. (2018) · PLoS ONE · doi:10.1371/journal.pone.0201715 · Cited by 51 · see citing works
The Impact of Message Mutation on the Fitness of a Genetic Code
Sella, G., & Ardell, D. H. (2002) · Journal of Molecular Evolution · doi:10.1007/s00239-001-0060-7 · Cited by 49 · see citing works
(1967) · doi:10.1016/s0079-6603(08)60951-4 · Cited by 48 · see citing works
Self-citationHirao, I., & Ellington, A. D. (1995) · Current Biology · doi:10.1016/s0960-9822(95)00205-3 · Cited by 48 · see citing works
On the Physical Basis of the Amino Acid Polar Requirement
Mathew, D. C., & Luthey-Schulten, Z. A. (2008) · Journal of Molecular Evolution · doi:10.1007/s00239-008-9073-9 · Cited by 47 · see citing works
Amino Acid Exchangeability and the Adaptive Code Hypothesis
Stoltzfus, A., & Yampolsky, L. Y. (2007) · Journal of Molecular Evolution · doi:10.1007/s00239-007-9026-8 · Cited by 45 · see citing works
A New Classification Scheme of the Genetic Code
Wilhelm, T. E., & Nikolajewa, S. (2004) · Journal of Molecular Evolution · doi:10.1007/s00239-004-2650-7 · Cited by 43 · see citing works
Tautomeric G•U pairs within the molecular ribosomal grip and fidelity of decoding in bacteria
Rozov, A., Wolff, P., Grosjean, H., Yusupov, M., Yusupova, G. Z., & Westhof, É. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky547 · Cited by 44 · see citing works
Giulio, M. D. (1996) · Origins of Life and Evolution of Biospheres · doi:10.1007/bf01808222 · Cited by 43 · see citing works
On the origin and evolution of the genetic code
Jim�nez-S�nchez, A. (1995) · Journal of Molecular Evolution · doi:10.1007/bf00173149 · Cited by 43 · see citing works
Guilt by association: The arginine case revisited
Knight, R. D., & Landweber, L. F. (2000) · RNA · doi:10.1017/s1355838200000145 · Cited by 43 · see citing works
Compartmentalization of amino acids in surfactant aggregates
Fendler, J. H., Nome, F., & Nagyváry, J. (1975) · Journal of Molecular Evolution · doi:10.1007/bf01732358 · Cited by 43 · see citing works
Evolution and multilevel optimization of the genetic codePreprint
Bollenbach, T., Vetsigian, K., & Kishony, R. (2007) · Genome Research · doi:10.1101/gr.6144007 · Cited by 43 · see citing works
A polyphyletic model for the origin of tRNAs has more support than a monophyletic model
Giulio, M. D. (2012) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2012.11.012 · Cited by 41 · see citing works
The rules of variation: Amino acid exchange according to the rotating circular genetic code
Castro-Chávez, F. (2010) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2010.03.046 · Cited by 39 · see citing works
Phenylalanine-Binding RNAs and Genetic Code Evolution
Illangasekare, M., & Yarus, M. (2002) · Journal of Molecular Evolution · doi:10.1007/s00239-001-0045-6 · Cited by 39 · see citing works
Sun, F.-J., & Caetano‐Anollés, G. (2008) · PLoS ONE · doi:10.1371/journal.pone.0002799 · Cited by 38 · see citing works
Symmetries of genetic code-doublets
Danckwerts, H.-J., & Neubert, D. (1975) · Journal of Molecular Evolution · doi:10.1007/bf01732219 · Cited by 38 · see citing works
Balasubramanian, R., Seetharamulu, P., & Raghunathan, G. (1980) · Origins of Life and Evolution of Biospheres · doi:10.1007/bf00928940 · Cited by 38 · see citing works
Di Giulio, M. (2016) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2016.04.005 · Cited by 34 · see citing works
The ocean abysses witnessed the origin of the genetic code
Giulio, M. D. (2005) · Gene · doi:10.1016/j.gene.2004.07.045 · Cited by 36 · see citing works
The coevolution theory of the origin of the genetic code
Giulio, M. D. (2004) · Physics of Life Reviews · doi:10.1016/j.plrev.2004.05.001 · Cited by 36 · see citing works
Origin of the genetic code: A physical-chemical model of primitive codon assignments
Nagyváry, J., & Fendler, J. H. (1974) · Origins of Life and Evolution of Biospheres · doi:10.1007/bf01207636 · Cited by 36 · see citing works
Stereospecificity of the genetic code
Melcher, G. (1974) · Journal of Molecular Evolution · doi:10.1007/bf01796558 · Cited by 35 · see citing works
The genetic code as a periodic table: algebraic aspects
Bashford, J. D., & Jarvis, P. (2000) · Biosystems · doi:10.1016/s0303-2647(00)00097-6 · Cited by 35 · see citing works
Codon Usage Decreases the Error Minimization Within the Genetic Code
Zhu, C.-T., Zeng, X., & Huang, W. (2003) · Journal of Molecular Evolution · doi:10.1007/s00239-003-2505-7 · Cited by 35 · see citing works
Natural history and experimental evolution of the genetic code
Wiltschi, B., & Budiša, N. (2007) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-006-0823-6 · Cited by 34 · see citing works
Giulio, M. D. (1995) · Origins of Life and Evolution of Biospheres · doi:10.1007/bf01582024 · Cited by 34 · see citing works
Protein structure prediction on the face centered cubic lattice by local search
Cebrián, M., Dotú, I., Hentenryck, P. V., & Clote, P. (2008) · National Conference on Artificial Intelligence · Cited by 33 · see citing works
Circular code motifs in the ribosome: a missing link in the evolution of translation?
Dila, G. K., Ripp, R., Mayer, C., Poch, O., Michel, C. J., & Thompson, J. (2019) · RNA · doi:10.1261/rna.072074.119 · Cited by 33 · see citing works
The Level and Landscape of Optimization in the Origin of the Genetic Code
Giulio, M. D., & Medugno, M. (2001) · Journal of Molecular Evolution · doi:10.1007/s002390010167 · Cited by 32 · see citing works
Butler, T., Goldenfeld, N. D., Mathew, D. C., & Luthey-Schulten, Z. A. (2009) · Physical Review E · doi:10.1103/physreve.79.060901 · Cited by 33 · see citing works
A statistical test of hypotheses on the organization and origin of the genetic code
Szathmรกry, E., & Zintzaras, E. (1992) · Journal of Molecular Evolution · doi:10.1007/bf00178593 · Cited by 30 · see citing works
Refactoring the Genetic Code for Increased Evolvability
Pines, G., Winkler, J. D., Pines, A., & Gill, R. T. (2017) · mBio · doi:10.1128/mbio.01654-17 · Cited by 29 · see citing works
A protein mapping method based on physicochemical properties and dimension reduction
Qi, Z., Jin, M., Li, S., & Feng, J. H. (2014) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2014.11.012 · Cited by 29 · see citing works
- Authors
- Woese, C. R., Dugre, D. H., Dugre, S. A., Kondo, M., & Saxinger, W. C.
- Affiliations
- University of Illinois Urbana-Champaign (US)
- Venue
- Cold Spring Harbor Symposia on Quantitative Biology
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 1966-01-01
- Volume
- 31
- Issue
- 0
- Pages
- 723-736
- ISSN
- 0091-7451 (ISSN-L)
- 1943-4456
- OpenAlex
- W2027298209
- Cited by
- 274
- References
- 0
- Citations by year
- 2026: 7 · 2025: 2 · 2024: 5 · 2023: 7 · 2022: 4 · 2021: 8 · 2020: 7 · 2019: 6 · 2018: 9 · 2017: 12 · 2016: 5 · 2015: 5 · 2014: 3 · 2013: 8 · 2012: 5
- Type
- posted content
- Language
- en
- Open access
- closed
- Locations
- Cold Spring Harbor Symposia on Quantitative Biology (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Physical Sciences › Physics and Astronomy › Astronomy and Astrophysics › Origins and Evolution of Life
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- genetic code, codon assignment, codon usage bias, gene transcription, translation (biology), in vitro translation system, genetic code evolution
- MeSH terms
- Amino Acids, Chemistry, Biological Evolution, Genetic Code, Models, Biological, Ribosomes, RNA, Transfer, Chemical Phenomena
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