Hierarchy of codon usage frequencies from codon-anticodon interaction in the crystal basis model.

Analyzing the codon usage frequencies of a specimen of 20 plants, for which the codon-anticodon pattern is known, we have remarked that the hierarchy of the usage frequencies present an almost "universal" behavior. Searching to explain this behavior, we assume that the codon usage probability results from the sum of two contributions: the first dominant term is an almost "universal" one and it depends on the codon-anticodon interaction; the second term is a local one, i.e. depends on the biological species. The codon-anticodon interaction is written as a spin-spin plus a z-spin term in the formalism of the crystal basis model. From general considerations, in particular from the choice of the signs and some constraints on the parameters defining the interaction, we are able to explain most of the observed data.

Codon bias from minimization of codon-anticodon interaction.

Inequalities between codon usage probabilities for quartets of codons are derived using a minimum principle for codon-anticodon interaction and a probability sum rule in the framework of the Crystal Basis Model of the genetic code. Performing this study separately for the Early and for the Eukaryotic Genetic Code, we observe a consistency in the obtained results for the two codes as well as a good agreement with data from Kasuza Codon Usage Database. Then we analyze the coherent changes of sign occurring, in the evolution from the Early to the Eukaryotic code, in the two parameters regulating the codon-anticodon interaction potential.

Codon-anticodon interaction and the genetic code evolution.

The evolution of the genetic code, with 20 amino acids encoded from the beginning, is analyzed from the viewpoint of codon-anticodon interaction. Imposing a minimum principle for the interaction, in the framework of the so called crystal basis model of the genetic code, we determine the structure of the anticodons in the ancient, archetypal and early genetic codes, that are all reconciled in a unique frame. Most of our results agree with the generally accepted scheme.

A minimum principle in codon-anticodon interaction.

Imposing a minimum principle in the framework of the so-called crystal basis model of the genetic code, we determine the structure of the minimum set of anticodons which allows the translational-transcription for animal mitochondrial code. The results are in very good agreement with the observed anticodons.

Universality and Shannon entropy of codon usage.

The distribution functions of codon usage probabilities, computed over all the available GenBank data for 40 eukaryotic biological species and five chloroplasts, are best fitted by the sum of a constant, an exponential, and a linear function in the rank of usage. For mitochondria the analysis is not conclusive. These functions are characterized by parameters that strongly depend on the total guanine and cytosine (GC) content of the coding regions of biological species. It is predicted that the codon usage is the same in all exonic genes with the same GC content. The Shannon entropy for codons, also strongly dependent on the exonic GC content, is computed.

Prediction of physical-chemical properties of amino acids from genetic code.

Using the crystal basis model of the genetic code, a set of relations between the physical-chemical properties of the amino acids are derived and compared with the experimental data. A prediction for the not yet measured thermodynamical parameters of three amino acids is done.

A minimum principle in mRNA editing?

mRNA editing of sequences of many species is analyzed. The nature of the inserted nucleotides and the position of the insertion sites, once fixed the edited peptide chain, are explained by introducing a minimum principle in the framework of the crystal basis model of the genetic code introduced by the authors.

Crystalizing the genetic code.

New developments are presented in the framework of the model introduced bythe authors in References [1, 2] and in which nucleotides as well ascodons are classified in crystal bases of the quantum group U(q)(sl(2) ⊕ sl (2)) in the limit q → 0. An operator whichgives the correspondence between the amino-acids and the codons isobtained for any known genetic code. The free energy released by basepairing of dinucleotides as well as the relative hydrophilicity andhydrophobicity of the dinucleosides are also computed. For the vertebrateseries, a universal behaviour in the ratios of codon usage frequencies isput in evidence and is shown to fit nicely in our model. Then a firstattempt to represent the mutations relative to the deletion of apyrimidine by action of a suitable crystal spinor operator is proposed.Finally recent theoretial descriptions are reviewed and compared with ourmodel.PACS number: 87.10.+e, 02.10.-v.

Implication of HLA-DMA alleles in corsican IDDM.

The HLA-DM molecule catalyses the CLIP/antigen peptide exchange in the classical class II peptide-binding groove. As such, DM is an antigen presentation regulator and may be linked to autoimmune diseases. Using PCR derived methods, a relationship was revealed between DM gene polymorphism and IDDM, in a Corsican population. The DMA*0101 allele was observed to confer a significant predisposition to this autoimmune disease while the DMA*0102 allele protected significantly. Experiments examining polymorphism of the HLA-DRB1 gene established that these relationships are not a consequence of linkage disequilibrium with HLA-DRB1 alleles implicated in this pathology. The study of the DMA gene could therefore be an additional tool for early IDDM diagnosis in the Corsican population.