Mots-Clés

database python PostgreSQL html

Description

Starting date: between February and June 2022

Research context

Type I Toxin-Antitoxin systems (T1TA) are self-death inducing 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 is able to activate the degradation and/or to inhibit the translation of the toxin mRNA. Specific structural features of the toxin mRNA were recently described allowing a tigh regulation of the toxin expression (1). T1TAs are involved in bacterial phage defense, persistence, and maintenance of mobile genetic elements. T1TAdb (2,3) 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

• Scanning selected bacterial genomes to identify T1TA homologs • Integrating T1TA homologs into the T1TAdb database

• Upgrading/migrating the T1TAdb database from Perl to Python

Skills

• Familiarized with command-line Linux • Programming with Python • Database management (MySQL, PostgreSQL)

• Web development (HTML, Javascript)

• 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) between January and December 2022. 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. More information about the ARNA lab can be found at https://arna.cnrs.fr/