Thesis: Circular code motifs in protein-coding genes and ribosomal RNAs

PhD defense: Gopal Krishna DILA

Title:  Circular code motifs in protein-coding genes and ribosomal RNAs

Team: CSTB

Abstract: The thesis focuses on motifs of the circular code X, an error-correcting code found in protein-coding genes, which have the ability to synchronize the reading frame. We first investigated the evolutionary conservation of X motifs in genes of different species and identified specific selective pressures to maintain them. We also identified a set of universal X motifs in ribosomal RNAs, which are located in important functional regions of the ribosome and suggest that circular codes represented an important step in the emergence of the standard genetic code (SGC). Then, we investigated the functional role of X motifs in modern translation processes and identified a strong correlation between X motif enrichment in genes and translation levels. Finally, we compared the frameshift optimality of the circular code X with the SGC and other maximal circular codes, and identified a new functionality of the code X in minimizing the effects of translation errors after frameshift events.

The jury is composed by M. MICHEL Christian (Professeur, Université de Strasbourg - thesis director), M. BERNOT Gilles (Professeur, Université de Nice Sophia Antipolis), Mme GASPIN Christine (Directeur de recherche, INRAE, Toulouse), Mme THOMPSON Julie (Directeur de recherche, Université de Strasbourg), M. POCH Olivier (Directeur de recherche, Université de Strasbourg), M. TIMSIT Youri (Directeur de recherche, Institut Méditerranéen d’Océanologie).

The defense will be held in English, on November 12th at 2pm in the Room 113, Forum, Faculty of Medicine, Strasbourg.

Keywords: circular code motifs, error-correcting code, standard genetic code, ribosomal RNA, reading frame, protein-coding genes, frameshift, translation errors