Genetic Code Optimization for Cotranslational Protein Folding: Codon Directional Asymmetry Correlates with Antiparallel Betasheets, tRNA Synthetase Classes
A new codon property, codon directional asymmetry in nucleotide content (CDA), reveals a biologically meaningful genetic code dimension: palindromic codons (first and last nucleotides identical, codon structure XZX) are symmetric (CDA = 0), codons with structures ZXX/XXZ are 5′/3′ asymmetric (CDA = ...
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| Format: | Article |
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Elsevier
2017-01-01
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| Series: | Computational and Structural Biotechnology Journal |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037017300636 |
| _version_ | 1818837261306822656 |
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| author | Hervé Seligmann Ganesh Warthi |
| author_facet | Hervé Seligmann Ganesh Warthi |
| author_sort | Hervé Seligmann |
| collection | DOAJ |
| description | A new codon property, codon directional asymmetry in nucleotide content (CDA), reveals a biologically meaningful genetic code dimension: palindromic codons (first and last nucleotides identical, codon structure XZX) are symmetric (CDA = 0), codons with structures ZXX/XXZ are 5′/3′ asymmetric (CDA = −1/1; CDA = −0.5/0.5 if Z and X are both purines or both pyrimidines, assigning negative/positive (−/+) signs is an arbitrary convention). Negative/positive CDAs associate with (a) Fujimoto's tetrahedral codon stereo-table; (b) tRNA synthetase class I/II (aminoacylate the 2′/3′ hydroxyl group of the tRNA's last ribose, respectively); and (c) high/low antiparallel (not parallel) betasheet conformation parameters. Preliminary results suggest CDA-whole organism associations (body temperature, developmental stability, lifespan). Presumably, CDA impacts spatial kinetics of codon-anticodon interactions, affecting cotranslational protein folding. Some synonymous codons have opposite CDA sign (alanine, leucine, serine, and valine), putatively explaining how synonymous mutations sometimes affect protein function. Correlations between CDA and tRNA synthetase classes are weaker than between CDA and antiparallel betasheet conformation parameters. This effect is stronger for mitochondrial genetic codes, and potentially drives mitochondrial codon-amino acid reassignments. CDA reveals information ruling nucleotide-protein relations embedded in reversed (not reverse-complement) sequences (5′-ZXX-3′/5′-XXZ-3′). Keywords: Secondary structure, Codon-amino acid assignment, Mitochondrial genetic code, Synonymous codon, Alpha helix, Beta turn |
| first_indexed | 2024-12-19T03:19:41Z |
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| id | doaj.art-7ace157e6a7949179c83f2a1fc1ed3f6 |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-12-19T03:19:41Z |
| publishDate | 2017-01-01 |
| publisher | Elsevier |
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| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-7ace157e6a7949179c83f2a1fc1ed3f62022-12-21T20:37:49ZengElsevierComputational and Structural Biotechnology Journal2001-03702017-01-0115412424Genetic Code Optimization for Cotranslational Protein Folding: Codon Directional Asymmetry Correlates with Antiparallel Betasheets, tRNA Synthetase ClassesHervé Seligmann0Ganesh Warthi1Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, Postal code 13385, France; Dept. Ecol Evol Behav, Alexander Silberman Inst Life Sci, The Hebrew University of Jerusalem, IL-91904 Jerusalem, Israel; Corresponding author at: Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, Postal code 13385, France.Aix-Marseille Univ, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM 63, CNRS UMR7278, IRD 198, INSERM U1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, Postal code 13385, FranceA new codon property, codon directional asymmetry in nucleotide content (CDA), reveals a biologically meaningful genetic code dimension: palindromic codons (first and last nucleotides identical, codon structure XZX) are symmetric (CDA = 0), codons with structures ZXX/XXZ are 5′/3′ asymmetric (CDA = −1/1; CDA = −0.5/0.5 if Z and X are both purines or both pyrimidines, assigning negative/positive (−/+) signs is an arbitrary convention). Negative/positive CDAs associate with (a) Fujimoto's tetrahedral codon stereo-table; (b) tRNA synthetase class I/II (aminoacylate the 2′/3′ hydroxyl group of the tRNA's last ribose, respectively); and (c) high/low antiparallel (not parallel) betasheet conformation parameters. Preliminary results suggest CDA-whole organism associations (body temperature, developmental stability, lifespan). Presumably, CDA impacts spatial kinetics of codon-anticodon interactions, affecting cotranslational protein folding. Some synonymous codons have opposite CDA sign (alanine, leucine, serine, and valine), putatively explaining how synonymous mutations sometimes affect protein function. Correlations between CDA and tRNA synthetase classes are weaker than between CDA and antiparallel betasheet conformation parameters. This effect is stronger for mitochondrial genetic codes, and potentially drives mitochondrial codon-amino acid reassignments. CDA reveals information ruling nucleotide-protein relations embedded in reversed (not reverse-complement) sequences (5′-ZXX-3′/5′-XXZ-3′). Keywords: Secondary structure, Codon-amino acid assignment, Mitochondrial genetic code, Synonymous codon, Alpha helix, Beta turnhttp://www.sciencedirect.com/science/article/pii/S2001037017300636 |
| spellingShingle | Hervé Seligmann Ganesh Warthi Genetic Code Optimization for Cotranslational Protein Folding: Codon Directional Asymmetry Correlates with Antiparallel Betasheets, tRNA Synthetase Classes Computational and Structural Biotechnology Journal |
| title | Genetic Code Optimization for Cotranslational Protein Folding: Codon Directional Asymmetry Correlates with Antiparallel Betasheets, tRNA Synthetase Classes |
| title_full | Genetic Code Optimization for Cotranslational Protein Folding: Codon Directional Asymmetry Correlates with Antiparallel Betasheets, tRNA Synthetase Classes |
| title_fullStr | Genetic Code Optimization for Cotranslational Protein Folding: Codon Directional Asymmetry Correlates with Antiparallel Betasheets, tRNA Synthetase Classes |
| title_full_unstemmed | Genetic Code Optimization for Cotranslational Protein Folding: Codon Directional Asymmetry Correlates with Antiparallel Betasheets, tRNA Synthetase Classes |
| title_short | Genetic Code Optimization for Cotranslational Protein Folding: Codon Directional Asymmetry Correlates with Antiparallel Betasheets, tRNA Synthetase Classes |
| title_sort | genetic code optimization for cotranslational protein folding codon directional asymmetry correlates with antiparallel betasheets trna synthetase classes |
| url | http://www.sciencedirect.com/science/article/pii/S2001037017300636 |
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