M2 - Ecological and evolutionary investigation of a new biosynthetic pathway involved in bacterial energy production with -omics data

Type de poste
Niveau d'étude minimal
Dates
Durée du poste
Contrat renouvelable
Contrat non renouvelable
Date de prise de fonction
Date de fin de validité de l'annonce
Localisation
Adresse

Institut Jean Roget - Domaine de la Merci
Université Grenoble-Alpes
38700 La Tronche
France

Contacts
Sophie Abby
Fabien Pierrel
Nelle Varoquaux
Email du/des contacts
sophie.abby@univ-grenoble-alpes.fr
fabien.pierrel@univ-grenoble-alpes.fr
nelle.varoquaux@univ-grenoble-alpes.fr
Description

Context:
Ubiquinone (UQ) is a lipid essential to electron transfer in respiratory chains that generate cellular energy in bacteria and eukaryotes. UQ production was so far known to generally depend on the presence of O2. We recently discovered a new biosynthetic pathway for O2-independent production of UQ [1]. This pathway was elucidated in Escherichia coli and its relevance for virulence suggested in Pseudomonas aeruginosa [2]. We showed that this pathway is scattered yet very widespread across UQ-producing Proteobacteria, including in many evolutionarily (close to the mitochondrial ancestor), clinically and industrially relevant strains. We now want to investigate the prevalence of this pathway in different types of environments in order to decipher its ecological and evolutionary relevance across a phylum emblematic of success in O2-rich environments.

Proposed work:
We propose to (i) mine publicly available data (genomes and metagenomes) for the presence of this pathway using annotation tools developed in the lab, and perform association studies with environmental meta-data (type of environments, including O2-levels) in an evolutionary framework. (ii) High UQ levels were previously reported but unexplained in O2-deprived water layers of the Black Sea (Figure 1) [3]. We propose to solve this issue by investigating possible associations between the presence of UQ (and other isoprenoid lipids) and their respective biosynthetic genes in these environments. This will be done by performing combined analyses of original lipidomics (lipids determination) and metagenomics data from samples we recently collected from the Black Sea water column.

Techniques:
During this project, the intern will create scripts and use programs to manipulate, assemble and analyse large and diverse –omics data (Python, R, BASH, awk…) in order to generate new insights on the ecophysiological role of UQ, a crucial molecule that appeared on Earth > 2 billion years ago [4].

Training environment:
We are part of a highly inter-disciplinary team, gathering biochemists, biophysicists, geneticists, biostatisticians and bioinformaticians, with a common strong interest in microbial evolution, making the GEM team a very rich training environment. The team is located on the Campus of La Tronche, in close vicinity to Grenoble city center (Tram B). https://www-timc.imag.fr/en/gem
Training starting date is flexible.

References:
[1] Pelosi L*, Vo CD* et al. (2019). Ubiquinone Biosynthesis over the Entire O2 Range: Characterization of a Conserved O2-Independent Pathway. MBio

[2] Vo CD*, Michaud J* et al (2020). The O2-independent pathway of ubiquinone biosynthesis is essential for denitrification in Pseudomonas aeruginosa. Journal of Biological Chemistry

[3] Becker KW*, Elling FJ* et al. (2018). Isoprenoid Quinones Resolve the Stratification of Redox Processes in a Biogeochemical Continuum from the Photic Zone to Deep Anoxic Sediments of the Black Sea. Applied Environmental Microbiology

[4] Abby et al. (2020). Advances in bacterial pathways for the biosynthesis of ubiquinone. Biochimica et Biophysica Acta (BBA)-Bioenergetics

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