MA/MSc Internship for EUGLOH program

Keywords: Transposable Element, Group II Intron Retrotransposon, Bacteria, Resistance to Phages, Stress-response

Internship Duration: 30/11/-1 - 30/11/-1

Transposable elements are genetic units that are capable of moving from one location to another in the genome. These mobile elements are present in all branches of the tree of life and play important roles in genome diversification and evolution. In addition, some transposable elements can drive adaptive evolution by providing their host organism with specific genetic and phenotypic characteristics that allow the host to adapt to stresses caused by environmental changes.
Transposable elements can be distinguished into "transposons" and "retrotransposons" according to their mobility mode. The genomic mobility of retrotransposons involves an RNA intermediate that is generated by transcription of the retrotransposon copy inserted in the genome.
Bacterial genomes contain different types of transposable elements and in the laboratory we employ a multidisciplinary approach combining genetics, genomics and biochemistry to study specific retrotransposable elements called ‘Group II Introns’, hereafter referred to as ‘G2I’. These G2I elements are widespread in bacteria and colonize genomes through a very sequence-specific mobility pathway called ‘Retrohoming’. Moreover, G2I retrotransposons have important biotechnological applications for the genetic engineering of bacterial genomes.
We are currently studying the biology of a specific family of G2I elements that are always inserted in genomes in very close proximity to essential protein-coding genes. Most of the genes targeted by these ‘specialized’ G2I elements play crucial roles in DNA metabolism, chromosomal replication/repair or in the bacterial stress-response. These particular genetic contexts clearly argue in favor of a selective advantage conferred by the G2I element to their bacterial host. Interestingly, we recently found that some of these ‘specialized’ G2I can confer to their bacterial host a better resistance to phage infection. These results rise the possibility that some G2I elements may act as anti-phage defense systems.
The goal of the internship is to continue the genetic and molecular study of these ‘specialized’ G2I elements. Using a combination of molecular biology, bacterial genetics and genomic approaches, we aim to characterize both their mobility pathway and their functional impact on bacterial physiology, stress-response and resistance to phage infections. For these purposes, different bacterial strains carrying in their genome engineered copies of specific G2I elements will be constructed and analyzed phenotypically in a variety of conditions, including stress and phage infection. In addition, RNA-seq and proteomic experiments will be carried out to analyze the impact of these G2I elements on the transcriptional and translational program of their neighboring genes.

Molecular biology techniques (PCR, cloning, plasmid and genomic DNA preparations). Bacterial genetics (growth curves, in vivo mobility assays, construction of bacterial strains, phenotypic tests). Genome-wide techniques (RNA-seq).

Lambowitz AM, Belfort M (2015) Mobile Bacterial Group II Introns at the Crux of Eukaryotic Evolution. Microbiol Spectr. 2015 Feb;3(1):MDNA3-0050-2014.
doi: 10.1128/microbiolspec.MDNA3-0050-2014

Enyeart PJ, Mohr G, Ellington AD, Lambowitz AM (2014) Biotechnological applications of mobile group II introns and their reverse transcriptases: gene targeting, RNA-seq, and non-coding RNA analysis. Mobile DNA. Jan 13;5(1):2.
doi: 10.1186/1759-8753-5-2

Monachello D, Lauraine M, Gillot S, Michel F, Costa M. A new RNA-DNA interaction required for integration of group II intron retrotransposons into DNA targets. Nucleic Acids Res. 2021 Dec 2;49(21):12394-12410. doi: 10.1093/nar/gkab1031.

• Pharmacy, Biology, Physics and Chemistry
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