Description of the thesis topic

A PhD student position is available in the Viral replicase structure and Function team at the AFMB laboratory (https://www.afmb.univ-mrs.fr/en/) (Aix Marseille Université and CNRS), in MARSEILLE France. The position will be fully funded by NidoRep, a European Research Council (ERC) seed grant led by Dr Ashleigh Shannon (Principal Investigator (PI)), with contracts managed by CNRS. The candidate will be co-supervised by Dr Bruno Canard The project will explore how distinct viruses of the order Nidovirales regulate viral replication at the structural and functional level. Nidovirales represent an intriguing group of RNA-positive viruses, whose genomes of various sizes (11-41 kb) reflect a long history of adaptation to specific niches. They remain largely neglected, with the exception of the large-genome (32 kb) Coronaviridae (CoV) family, which includes the famous human pathogen SARS-CoV-2. At the other end of the size spectrum is the small-genome (11 kb) Arteriviridae (ArV) family, a little-studied group of prevalent pathogens that infect animals and pose a significant threat of spread to humans. NidoRep aims to decipher the structural and functional evolution of viral enzymes specific to the CoV and ArV families. It will focus in particular on the viral transcription and replication complex (RTC), at the heart of which lies RNA polymerase and its unique N-terminal domain, known as NiRAN.

Work Context

AFMB is a structural biology and proteomics research center, composed of five distinct research teams and supported by state-of-the-art technical platforms and various services, including parallel and robotic cloning, expression, purification and crystallization, cryo-EM, bioinformatics, antiviral screening, and drug design and synthesis. Candidates will form a team comprising two PhD students, a post-doc, a research technician (engineer) and the principal investigator (Ashleigh Shannon), as part of Dr Bruno Canard's wider Viral Replicases: Structure, Function and Drug Design team. As such, they will have access to additional specialized equipment for the study of viral enzymes required for the planned research, including a radioactivity laboratory, sequencing devices and various biochemical equipment for measuring enzyme activity.
We are looking for highly motivated, collaborative individuals who are keen to improve their knowledge in the fields of structural biology and biochemistry. The project will include cloning, mutagenesis, protein expression and purification, and functional activity studies with purified proteins, as well as structural characterization by crystallography or CryoEM (platforms available on site). Functional studies may include work with radioactivity (H3, P32), which is carried out in an L2 laboratory, subject to restrictions (medical examination and prior authorization). Specific requirements - Master's degree or equivalent (in structural biology, molecular biology, biochemistry or a related field). - Basic knowledge and experience in crystallography or CryoEM (or SAXS). - Experience in DNA/RNA manipulation (cloning, mutagenesis, PCR). - Experience of protein expression and purification, preferably using a bacterial system (E.coli). - Knowledge of other chemistry/biochemistry techniques, such as LC/MS, SEC-MALS, co-immunoprecipitation, cross-linking, western blots, ITC, BLI, MST, is highly desirable. - Good oral and written communication skills in English and/or French.

Constraints and risks

Part of the screening platform's equipment is located in a type L2 laboratory, where radioactivity (H3, P32) is handled, and access to which is subject to restrictions (medical examination and prior authorization). The laboratory is also GMO/MOT-accredited. The PhD student must be able to meet these accreditation criteria even if he/she will not be handling radioactivity and/or MOTs. Because of the specific equipment required to carry out the activity, teleworking is not eligible.