3-year postdoctoral position in enzymology: characterization of putative novel CAZyme families

RESEARCHER PROFILE: Postdoc / R2: PhD holders

RESEARCH FIELD(S) AND DISCIPLINES1: Biology/Chemistry: Biochemistry, Catalysis, Glycobiology

JOB /OFFER DESCRIPTION:

Host Institute/Group

The candidate will join 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.

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 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. 

WHAT WE OFFER:

The salary (after deduction of taxes) ranges from 2050€ to 2400€ depending on the experience (< or > 3 years after the PhD degree) and increased by 250€ after one year. 

The CAZy database/bioinformatics is a hub in the community, for decades, hence joining our group would provide an opportunity to be introduced in a large network of biochemist collaborators, from those involved in these project (BBF, CERMAV, SBR) to worldwide during dedicated conferences such as the biennial Gordon Research Conference and Carbohydrate Bioengineering Meeting.

TYPE OF CONTRACT: TEMPORARY / JOB STATUS: FULL TIME / HOURS PER WEEK: 35

JOB FUNDED THROUGH AN EU RESEARCH FRAMEWORK PROGRAMME

APPLICATION DEADLINE: 31/08/2023 

ENVISAGED STARTING DATE: 01/10/2023 

ENVISAGED DURATION: 42 months

WORK LOCATION(S): Architecture and Functions of Biological Molecules - AFMB Lab - (affiliated to Aix-Marseille Université, CNRS, INRAE) laboratory, Campus Luminy (Luminy campus, in the Calanques National Park), 13009 Marseille, France

QUALIFICATIONS, REQUIRED EDUCATION LEVEL, PROFESSIONAL SKILLS, RESEARCH REQUIREMENTS 

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, as described in: 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.

SOFT SKILLS: Autonomy, Organization, Communication in English.

REQUESTED DOCUMENTS OF APPLICATION, SELECTION PROCESS: 

Curriculum and cover letter

WHERE TO APPLY: nicolas.terrapon@univ-amu.fr