Mots-Clés

bioinformatics, python, SQL

Description

Research context

Type I Toxin-Antitoxin systems (T1TAs) are suicide systems expressed by bacteria consisting of two genes: a stable toxin and an unstable antitoxin that neutralizes the action of the toxin. In these systems, the RNA antitoxin inhibits the translation of the toxin mRNA or leads to its degradation. T1TAs are involved in maintenance of mobile genetic elements, bacterial phage defense and persistence. To avoid unwanted toxicity, the expression of the toxin is also tightly regulated by structural features1.

T1TAdb2,3 is a database of all described and predicted loci of type I Toxin-Antitoxin systems3. This database provides sequence, secondary structure, and genomic information on T1TA loci. It currently contains 1894 Toxin-Antitoxin loci from 493 bacterial strains and 25 TA families.

1 https://journals.asm.org/doi/10.1128/microbiolspec.RWR-0030-2018

2 https://d-lab.arna.cnrs.fr/t1tadb             

3 https://rnajournal.cshlp.org/content/early/2021/09/16/rna.078802.121

Tasks

• Annotating novel T1TA homologs
• Integrating T1TA homologs into the T1TAdb database
• Improving the T1TAdb database features (Python)

Skills

• Familiarized with command-line Linux

• Programming with Python
• Database management (MySQL, PostgreSQL)
• Web development (HTML, Javascript, Django)
• Producing and maintaining reliable, reproducible, and documented work

Work environment

The work will be carried out in the ARNA Laboratory “Nucleic acids: Natural and artificial regulation” (Inserm U1212, CNRS UMR 5320, University of Bordeaux, France). ARNA is an interdisciplinary unit gathering around 120 chemists, biologists, and biophysicists studying nucleic acids. The bioinformatician will join the BacRB team, focusing on the regulation of type I toxin-antitoxin systems in bacterial pathogens. https://lerhun.u-bordeaux.fr/