Post-Doctoral Fellowship Position in CAZy
Functional characterization of carbohydrate-active enzyme
Location : Aix-Marseille University (Luminy campus), FRANCE
Host Institute/Group
The candidate will join the Glycogenomics group in the AFMB laboratory (Architecture et Fonction des Macrolécules Biologiques; www.afmb.univ-mrs.fr/?lang=en) at Marseille, France. AFMB is located on the Luminy campus, in the middle of the Calanques National Park next to the Mediterranean Sea, and is jointly affiliated to CNRS (https://www.cnrs.fr/en) and Aix-Marseille University (www.univ-amu.fr/en). The AFMB lab is specialized in the structural and functional characterization of biological macromolecules, with Virology and Glycobiology as main themes. The laboratory is fully equipped for the production and purification of recombinant proteins (in prokaryotic as well as in eukaryotic systems), biophysical characterizations, crystallization, x-ray diffraction, etc.
The Glycogenomics group, created by Bernard Henrissat and now led by Nicolas Terrapon, gathers bioinformaticians and wet-lab biologists to maintain and develop the CAZy database (Carbohydrate Active EnZymes; www.cazy.org) launched in 1998. CAZy has become the world reference classification of enzymes involved in glycan assembly and breakdown, not only due to the high specificity of these enzymes but also by the involvement of the CAZy team in data curation and extraction of up-to-date functional information. Glycan breakdown is central to human and animal nutrition, fungal/plant-cell wall remodeling, biomass re-utilization, host-pathogen interactions, etc. In the era of high-throughput sequencing, CAZy is thus an essential resource for the functional readability of genomes and metagenomes in their use of the diverse glycans as energy source. Such analyses feed the CAZy system that now exploits this large amount of data by comparative genomics approaches to actively participate in enzyme discovery.
Work context
A post-doctoral position is open now in the context of the funded project ODE, for Operon-based Discovery of carbohydrate-active Enzymes (350k€ attributed to Nicolas Terrapon by the French Research Agency, ANR). The aim of this project is to boost the discovery of enzyme families involved in glycan breakdown. To do so, operons for glycan breakdown in the Bacteroidetes phylum, referred as to PULs (Polysaccharide Utilization Loci), are currently analyzed at large scale to identify protein of unknown that are the best candidates of new CAZy families, and to deduce their most likely substrate. Approximatively 200 targets from 40 distinct families will be selected, synthetic genes will be ordered, and proteins produced/purified by the high-throughput recombinant protein production platform of the AFMB lab. The main task of the recruited fellow will be to enzymatically characterize these putative CAZymes. The contract could start between September 2021 and January 2022, and will run for 2 years.
Technical Skills
The wet-lab part of the ODE project will be supervised by Marie-Line Garron, structural biologist in the Glycogenomics team and Assistant Professor at Aix-Marseille University. The work features two components:
- The first is the production/purification of the soluble selected targets in sufficient yield. To perform this work, the candidate needs to be comfortable with high-throughput techniques, and knowledge in TECAN robot system (Freedom EVO200) would be an advantage. The applicants should have a solid experience in the biochemistry techniques for recombinant proteins, mainly from prokaryotes, but experience in eukaryotic proteins will be appreciated. Indeed, part of the targets will be selected in fungal genomes and analyzed in collaboration with Jean-Guy Berrin’s group at the Fungal Biodiversity and Biotechnology laboratory of INRAE (www.inrae.fr/en), located 200m away from the AFMB lab on the Luminy campus.
- The second task will be to develop automated screening protocols for enzyme functional characterization at AFMB, similar to those described in www.pnas.org/content/116/13/6063. These protocols were developed by close collaborators in William Helbert’s group at the CERMAV laboratory (Grenoble, FRANCE), hence a 6-month stay in Grenoble is budgeted in the ODE project grant for technical transfer. For this task, the applicant will also collaborate with Renaud Vincentelli, leader of the high-throughput protein production platform at AFMB.
The candidate must have documented experience in enzymology and enzyme kinetics. Previously acquired knowledge specific to the enzymology of CAZymes such as substrates detection by colorimetry, amperometry (HPAE-PAD Dionex) or NMR will be an advantage. All additionally skills in biophysics or structural biology, as mass spectrometry or crystallography, and of course, general glycobiology experience will be relevant as well.
posted March 24, 2021
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