3-year doctoral position in bioinformatics: Prediction of bacterial operons dedicated to glycan breakdown in marine Gammaproteobacteria for the discovery of novel CAZyme families (Funded by A*Midex)

RESEARCHER PROFILE: PhD/ R1: First stage Researcher                  
RESEARCH FIELD(S) AND DISCIPLINES1: Bioinformatics
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. The group gathers bioinformaticians and wet-lab biologists to maintain and develop the Carbohydrate Active EnZymes database, aka CAZy [1]. 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.

[1] Drula E, Garron ML, Dogan S, Lombard V, Henrissat B, Terrapon N. The carbohydrate-active enzyme database: functions and literature. Nucleic Acids Res. 2022 Jan 7;50(D1):D571-D577. PMCID: PMC8728194

Work context
A doctoral position in bioinformatics is opened in the context of the GOALS project, for Gammaproteobacteria Operons for polysaccharide utilization: from Algae to a Larger Scope (recently funded by Aix-Marseille University with 330k€ over 2023-2027). The final objective of this project is to characterize proteins of unknown function to become the founding members of novel Carbohydrate-Active enZyme (CAZyme) families. 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, attracted the attention of the community in the past decade, leading us to create a PUL prediction algorithm and associateddatabase (PULDB) [2-3], a spin-off of the CAZy database/website.

Recently, several publications reported that some Gammaproteobactia, notably within the Alteromonadales order (highly prevalent in marine ecosystems), also display operonic enzyme arsenals for the breakdown of polysaccharides. It is thus timely to unveil the propancy of marine Gammaproteobacteria to use operons for polysaccharide utilization. In the GOALS project, we first want to develop a PUL prediction algorithm specific to marine Gammaproteobacteria, as these do not display the same features as in Bacteroidota. We then want to implement a bioinformatic strategy to identify protein families of unknown function and to prioritize the best candidates, as this analysis should result in ordering synthetic genes for future wet-lab studies. 

[2] Terrapon, N., Lombard, V., Gilbert, H.J. and Henrissat, B.. Automatic prediction of polysaccharide utilization loci in Bacteroidetes species from the human gut microbiota. Bioinformatics 2015, 31(5):647-55. PMID: 25355788

[3] Terrapon N, Lombard V, Drula É, Lapébie P, Al-Masaudi S, Gilbert HJ, Henrissat B. PULDB: the expanded database of Polysaccharide Utilization Loci. Nucleic Acids Res. 2018, 4;46(D1):D677-D683. PMCID: PMC5753385

WHAT WE OFFER:
The salary (after deduction of taxes) will be from 1690€ to 1850€, following the ongoing increase of PhD salaries by Aix-Marseille University. 

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 collaborators, from those involved in the project, the collaboration with the Station Biologique de Roscoff, to worldwide during dedicated conferences such as the biennial Gordon Research Conference and Carbohydrate Bioengineering Meeting.

Additional information: The Euraxess Center of Aix-Marseille Université informs foreign visiting professors, researchers, postdoc and PhD candidates about the administrative steps to be undertaken prior to arrival at AMU and the various practical formalities to be completed once in France: visas and entry requirements, insurance, help finding accommodation, support in opening a bank account, etc. More information on AMU EURAXESS Portal 

TYPE OF CONTRACT: TEMPORARY / JOB STATUS: FULL TIME/ HOURS PER WEEK: 35
JOB NOT FUNDED THROUGH AN EU RESEARCH FRAMEWORK PROGRAMME                      
APPLICATION DEADLINE: 31/07/2024 
ENVISAGED STARTING DATE: 1/09/2024
ENVISAGED DURATION: 36 months

WORK LOCATION(S): The Architecture and Functions of Biological Molecules (AFMB Lab) laboratory in Marseille (France) is located on the Luminy campus, in the Calanques National Park. It is affiliated to Aix-Marseille Université, CNRS and INRAE institutes.

QUALIFICATIONS, REQUIRED EDUCATION LEVEL, PROFESSIONAL SKILLS, RESEARCH REQUIREMENTS 
The applicant should have achieved a Master degree in bioinformatics, with demonstrated experience in the analysis of genomic regions and protein sequences, and hence good knowledge of file formats and associated tools. The applicant should show strong programmatic skills, including scripting (Python, R), web (PHP, Javascript) and software development (GIT, reproducible science).

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