ArticleComputational and structural biotechnology journal2017
Genetic Code Optimization for Cotranslational Protein Folding: Codon Directional Asymmetry Correlates with Antiparallel Betasheets, tRNA Synthetase Classes.
Article in Computational and structural biotechnology journal, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed, 40 citations in OpenAlex.
- Mechanisms governing codon usage bias and the implications for protein expression in the chloroplast of Chlamydomonas reinhardtii.The Plant journal : for cell and molecular biology · 2022Review
- On the Evolutionary History of the Twenty Encoded Amino Acids.Chemistry (Weinheim an der Bergstrasse, Germany) · 2022Review
- Analysis of codon usage patterns in open reading frame 4 of hepatitis E viruses.Beni-Suef University journal of basic and applied sciences · 2022Article
- Genome Evolution from Random Ligation of RNAs of Autocatalytic Sets.International journal of molecular sciences · 2021Article
- Network analysis of synonymous codon usage.Bioinformatics (Oxford, England) · 2020Article
- First arrived, first served: competition between codons for codon-amino acid stereochemical interactions determined early genetic code assignments.Die Naturwissenschaften · 2020Article
- RNA Rings Strengthen Hairpin Accretion Hypotheses for tRNA Evolution: A Reply to Commentaries by Z.F. Burton and M. Di Giulio.Journal of molecular evolution · 2020Article
- Pentamers with Non-redundant Frames: Bias for Natural Circular Code Codons.Journal of molecular evolution · 2020Article
- The primordial tRNA acceptor stem code from theoretical minimal RNA ring clusters.BMC genetics · 2020Article
- Codon Directional Asymmetry Suggests Swapped Prebiotic 1st and 2nd Codon Positions.International journal of molecular sciences · 2020Article
- COSMO: A dynamic programming algorithm for multicriteria codon optimization.Computational and structural biotechnology journal · 2020Article
- The Alanine World Model for the Development of the Amino Acid Repertoire in Protein Biosynthesis.International journal of molecular sciences · 2019Review
- Article
- Theoretical minimal RNA rings designed according to coding constraints mimic deamination gradients.Die Naturwissenschaften · 2019Article
- Two Old Dogs, One New Trick: A Review of RNA Polymerase and Ribosome Interactions during Transcription-Translation Coupling.International journal of molecular sciences · 2019Review
- Chimeric Translation for Mitochondrial Peptides: Regular and Expanded Codons.Computational and structural biotechnology journal · 2019Article
- Bijective codon transformations show genetic code symmetries centered on cytosine's coding properties.Theory in biosciences = Theorie in den Biowissenschaften · 2018Article
- Protein Sequences Recapitulate Genetic Code Evolution.Computational and structural biotechnology journal · 2018Article
- Stem-Loop RNA Hairpins in Giant Viruses: Invading rRNA-Like Repeats and a Template Free RNA.Frontiers in microbiology · 2018Article
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Authors and funding
2 authors at 1 institution in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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').
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