Three-year postdoctoral position in enzymology : characterization of putative novel CAZyme families
- Work context
A postdoctoral position in biochemistry/enzymology is opened in the context of two funded projects, both aiming at characterizing proteins of unknown function which would become the founding members of novel Carbohydrate-Active enZyme (CAZyme) families. These projects are named Operon-based Discovery of carbohydrate-active Enzymes (ODE ; 350k€ funded by the French National Research Agency over 2020-2024) and Gammaproteobacteria Operons for polysaccharide utilization : from Algae to a Larger Scope (GOALS ; 330k€ recently funded by Aix-Marseille University over 2023-2027).
Our objective is to boost the discovery of CAZyme families by exploiting bacterial operons dedicated to glycan breakdown. These operons, referred to as Polysaccharide Utilization Loci (PUL) in the Bacteroidetes phylum, have attracted the attention of the community in the past years, leading us to create the PUL DataBase (PULDB), a spin-off of the CAZy database/website.
During the ODE project, we developed a bioinformatic strategy to identify protein families of unknown function, and used several indicators to rank/prioritize the best candidates for becoming novel CAZy families. Approximately 200 synthetic genes from 50 distinct candidate families have been ordered and partly processed by the high-throughput protein production/purification platform at the AFMB laboratory. Functional screening and some enzymatic characterizations were initiated by a postdoctoral fellow who will leave soon. The mission of the recruited fellow will be to pursue the enzymatic characterizations of proteins with positive screening results.
With the GOALS project, we will extend our scope beyond the Bacteroidetes phylum to marine Gammaproteobacteria. It will involve the development of a method to predict their specific PULs by the bioinformaticians in the team, in collaboration with people from the Marine Biology group in the Station Biologique de Roscoff for the generation of transcriptomics data. We will then select 100 more gene targets from candidate families and the recruited postdoctoral fellow will similarly lead the screening tests and functional characterization of the most relevant/positive results.
The contract should start as soon as possible, October 2023 the latest, and could run for 3.5 years. French postdoc positions involve 35h/week working and a salary (after deduction of taxes) ranging from 2050€ to 2400€ depending on the level of experience (if >3 years after PhD) and increased by 250€ after the first year.
- Host Institute/Group
The candidate will join the Glycogenomics group of the AFMB laboratory in Marseille, France. The laboratory is located on the Luminy campus, in the middle of the Calanques National Park, and belongs to the Aix-Marseille University. This laboratory specialized in the structural and functional characterization of biological molecules, mainly for Virology and Glycobiology. The laboratory is fully equipped for the production and purification of recombinant proteins (in prokaryotic as well as in eukaryotic systems), enzymatic assays, biophysics characterization, crystallization, etc.
The Glycogenomics group, created by Bernard Henrissat in 1998 and led by Nicolas Terrapon since 2019, gathers bioinformaticians and wet-lab biologists to maintain and develop the Carbohydrate Active EnZymes database, aka CAZy. CAZy is the worldwide reference classification of enzymes involved in the glycan assembly and breakdown, thanks to the high specificity of these enzymes but also to our involvement in human curation of sequence and literature data. Glycan breakdown is central to human and animal nutrition, fungal/algal/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 diverse energy sources. Such analyses fed the CAZy classification that now exploits this large amount of data by comparative genomics approaches to actively participate in novel enzyme discovery.
- Technical Skills
The applicants should have a solid experience in biochemistry techniques detailed below.
While the production/purification of the soluble proteins will be realized in collaboration with the high-throughput protein production/purification platform at the AFMB laboratory, an experience with high-throughput techniques with a TECAN robot system (Freedom EVO200) and chromatography techniques (using FPLC AKTA systems) would be an advantage. Knowledge in manipulation of eukaryotic proteins could also be appreciated as fungal targets can be produced in collaboration with the BOOST group led by Jean-Guy Berrin in the Fungal Biodiversity and Biotechnology (BBF)laboratory, located on Luminy Campus too.
The applicants should be able to design enzymatic assays and run screening protocols for enzyme functional characterization at AFMB, similar to those described in the publication : https://www.pnas.org/content/116/13/6063. These protocols were developed by close collaborators in William Helbert’s group at CERMAV (Grenoble), hence a stay in its group could be organized. Knowledge in enzymology such as carbohydrate detection by colorimetry, amperometry (HPAEC-PAD Dionex) or NMR, and calculation of catalytic constants, will be an advantage. However, the candidate will have the possibility to be trained on the whole process in particular on the design of enzymatic assays and on the detection of carbohydrates for enzyme characterization activity.
All additional skills in biophysics or structural biology, such as mass spectrometry, substrate-enzyme modeling or crystallography, could be taken into account.
- Contacts
Please reach nicolas.terrapon@univ-amu.fr providing your curriculum and a cover letter.