A Theoretical Approach for the Genetic Code

Paul SORBApaul.sorba@lapth.cnrs.fr

Seminar dedicated to my always young friend Branko

Belgrad, Sept.2015

Herceg-novi ‘68

Plan

• 1- A brief survey on the Genetic Code

• 2- Crystal basis model of G.C.

• 3- Codon-anticodon interaction and Applications:selection of anti-codon and evolution of the G.C.

work in collaboration with A.Sciarrino, Università di Napoli

- BioSystems 2012,107,p.113-119; ibid 2013,111,p.175-180, and preprint LAPTH-09/15, to appear in BioSystems- Review in p-Adics Numbers, Ultrametric analysis and Applications 2014, 6, p.257-274.

1- Genetic Code: a brief survey

The transmission of information from DNA (formed by 4 bases

C,G,A,T) (nucleotides) to protein building is a complex process of

transcription and translation.

From mRNA to tRNA and Amino acid

Standard Genetic Code

2- Crystal Basis Model of G.C.

• Applications of this model provided in a series of papers (L.Frappat, A.Sciarrino and P.S.) in the years 1998-2005. Among them:

• Study of codon usage probabilities, elaboration of sum rules.

• Relations between physico-chemical properties of amino-acids (a.a.) and predictions.

• More mathematical aspects: operator relating a.a. and codons for any known genetic code; attempts to describe mutations,etc.

3- Codon-anticodon Interaction

3a- Selection of anticodon in Mitochondrial Code

In VertebralMitochondrial

Code:

most used anticodons for mitochondria of animals

(Sprinzl et al, 1998)

As a first Conclusion

• Anticodons minimizing the conjectured operator Taver in very good agreement with the observed ones for mitochondria of animals.

• Results depending only of the sign of two coupling constants.• One may expect a more complicated pattern in the general

case, following the biological species. Might happen that the « universal » feature of Cv and CH should be released and T expressions modified.

• Then the crystal basis offers a lot of possibilities, for ex. adjunction of a term of « spin-spin » interaction of the type:

3b- Evolution of the Genetic Code

The genetic code has undergone an evolutionary process

- An evolutionary theory is the « codon capture theory »(review Ohama et al. (2008)):. number of the encoded amino acids is kept constant, equal to 20.. the coding codons change, key role in this process being played by the anticodon. In this context, 3 main codes: the Ancient and Early Codes, and an alternative: the Archetypal Code.

Ancient Code

Archetypal Code

EarlyCode

Mitochondrial Code

Standard Code

TIME

In ourmodel

A comparison and a propositionDifferences:

• In Ancient code, 20 codons and 20 anti-codons.• In Early code, all codons involved and 20 anti-codons.• In Archetypal code, all codons but 16 anticodons .

A proposal: Minimisation Conjecture in following way:

- T (anticodon-codon) in Ancient Code :with Watson-Crick pairing between nucleotids (i.e. C-G , U-A)

-T aver(anticodon-codon) in Archetypal and Early Codeswith « wobble » mechanism.

The case of Standard Genetic CodeAccording to the most accepted scheme, the three codon ending withW= C,U,A are read by the same anticodon starting with A, and the one

ending with G by the anticodon starting with C.

Two remarks in the evolution Early towards Standard Genetic Code

1- It is interesting to note that our minimization select the right anticodon proposed by the accepted scheme.

2- Taking a close look at the variation of the cH and cV parameters from the Early Code, (where, for each quartet of codons, cH is positive and cV negative) to the Eukaryotic –or Standard - Code, one remarks the same scenario for each quartet of codons, with a coherent change of sign in the two parameters regulating the evolution.

As a second Conclusion

• The « constants » Cv and CH deserve a more precise study. Their branching points would correspond to the advent of different Genetic Codes, with the standard G.C. emerging as the one exhibiting selective advantages.

• Could we verify that the existing G.C., that is the branching point which has survived, satisfies the required optimality conditions?

3c- Codon Bias

- Codon usage bias = Some codons are used much more frequently than others. We will consider our minimisation procedure to compare the probabilities of usage of codons relative to each amino-acid (relative to quartets and sextets).

Comparison of probabilities from minimization in Eukariotic Code

Comparing with data: very satisfying

• Examining the averaged codon frequencies over 48 biological species belonging to vertebrates (VRT), 73 to plants (PLN), 39 to invertebrates (INV), and 93 to bacteria (BACT):

Summary

• The evolution of the Genetic Code is analysed from the view-point of the codon-anticodon interaction.

• Imposing a Minimum principle for the Interaction, we determine, in the framework of the Crystal Basis Model, the structure of anticodons in the Ancient, Archetypal Early and finally Standard Genetic Codes, that are all reconciled in an unique frame.

• The above obtained results, joined to previous ones, encourage us to introduce the notion of « BIO-SPIN » related to the Uq(SU(2)+SU(2)) group of our model.

Outlooks

1- Enlargement of the Crystal Basis Model?

2- Program for a more detailed study of codon-anticodon interaction ( refinement of the interaction, more precise analysis following different species, impact on proteins…).3- Study of mutations…