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Functional characterization of de novo genes by genetic code expansion

Functional characterization of de novo genes by genetic code expansion

By In Aiv Internship On May 29, 2018


Internship title: Functional characterization of de novo genes by genetic code expansion

LABORATORY
Name: Laboratory of Computational and Quantitative Biology – Equipe Biologie des Génomes
Affiliation: Sorbonne Université – CNRS
Address: nstitut de Biologie Paris Seine, 7-9 Quai Saint Bernard Bâtiment C, 3ème étage, 75252 Paris Cedex 05
E-mail: gilles.fischer@sorbonne-universite.fr

LAB Director
Name: Alessandra Carbone
Phone number: +33144277345
E-mail: Alessandra.Carbone@lip6.fr

SUPERVISOR
Name: Gilles Fischer (head of the team Biology of Genomes)
Phone number: +33144278139
E-mail: gilles.fischer@sorbonne-universite.fr

Subject Keywords: Evolution, de novo genes, genome editing, Saccharomyces cerevisiae
Tools and methodologies: CRISPR-Cas9, Genetic Code Expansion, FACS, microbiology, phenotyping, protein purification
Summary of lab’s interests: Our research projects aim at understanding the biology and the evolution of eukaryotic genomes. We are combining an experimental approach on yeast species based on molecular genetics and functional genomics to an analytical exploration of genome sequences requiring bio-informatic skills and the development of new tools.
Project summary: It has long been thought that the emergence of totally new genes from non-coding sequences was impossible. However, more recent works demonstrated the emergence of completely new genes in many species but their role in adapting new species is still poorly understood. We recently identified about a hundred potential de novo genes in the genome of Saccharomces cerevisiae. We propose to use an innovative approach of synthetic biology call genetic code expansion to purify the translation products of these novel genes and to characterize their function. This approach involves site-specific incorporation of Unatural Amino Acids (Uaas) into neoproteins. The experimental approach is based on the combined use of a modified aminoacyl-tRNA synthetase (aaRS) and a suppressor tRNA to specifically insert a Uaa at a stop codon placed at a defined site in the sequence of neo-genes. The stop codons are introduced by the use of the CRISPR/Cas9 editing system and no change in the regulation of gene expression is induced. Site-specific incorporation of the Uaa called AzF will be used as a non-disruptive chemical probe for the purification of neoproteins and to identify known interacting partners to approach the de novo gene functions.
Interdisciplinary aspect of the project: This project is combining synthetic biology (genetic code expansion), genome editing (CRISP-Cas9), large-scale phenotyping, classical genetics, and biochemistry. Depending on the computational skills of the applicant, a bioinformatics aspect can be added to the internship through the exploration of the conservation of the de novo gene candidates at the population level.