Thesis: Circular codes in the evolution of the genetic code

PhD defense: Martin STARMAN

Title: Circular codes in the evolution of the genetic code

Team: CSTB

Abstract: The problem that this work addresses is how to retrieve, maintain and synchronize the correct reading frame during the translation process in the ribosome. Translation is the process by which the ribosome decodes the messenger RNA (mRNA a sequence of nucleotides {A, C, G, T}) as codons (words of 3 nucleotides) to create a specific amino acid chain that later folds into a protein. Unfortunately, the mRNA can be decoded in three reading frames 0, +1 and +2. Yet, only frame 0 as correct reading frame encodes the Information for the synthesis of proteins. Usually, the correct reading frame is indicated by a start signal. First practical evidence of a genetic model which is able to retrieve the correct reading frame is the so-called X-code. The X-code is a set of 20 codons that was discovered by a statistical analysis of genes of different species. Concatenations of words of this code appear preferentially in genes in frame 0. Such a concatenation is called a motif. In this thesis, mathematical models from graph theory, code theory and combinatorics are used to reconstruct a hypothetical course of such codes in the evolutionary development of the genetic code. These results should help as a guide in the development of a model of the evolution. With such a model, evolution can possibly be traced back to its origins.

The jury is composed by:

• Prof. C. Michel, Université de Strasbourg, Laboratoire ICube, directeur de thèse
• Prof. L. Strüngmann, Institut de mathématiques, Mannheim, Allemagne, co-directeur de thèsProf. A. Denise, Université Paris-Saclay, rapporteur
• Prof. S. Giannerini, Université de Bologne Italie, rapporteur
• Prof. E. Fimmel, Institut de mathématiques, Mannheim, Allemagne, examinateur
• Dr. J-S. Sereni, Laboratoire ICube, Strasbourg, examinateur

The defense will take place on Friday the 11th of December at 14:00 online.