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ESR-10 Viral enzymes in the Coronavirus RNA replication complex: assembly, mechanism, and inhibition (AMU)

Project description
The coronavirus (CoV) family contains important respiratory and enteric pathogens. The successive emergence of highly pathogenic CoVs such as the Severe Acute Respiratory Syndrome (SARS-CoV) in 2003 and the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) in 2012 highlights their zoonotic potential. To date, there is no treatment against CoVs.
In the lab we recently identified and characterized a highly active and processive SARS-CoV polymerase complex in vitro (Subissi et al., PNAS, 2014). We also demonstrated that the viral 3’-5’ exonuclease (ExoN) can excise mismatches generated by the polymerase complex (Bouvet et al., PNAS, 2012). This proofreading system is an unprecedented discovery in RNA viruses and would explain the inefficiency of Ribavirin (a nucleotide analogue) treatment in SARS- and MERS-patients.
Goals of the ESR will be to

  1. unravel nucleotide polymerisation mechanisms at the molecular and atomic level
  2. identify nucleotide analogues that are efficiently incorporated by the SARS-CoV and MERS-CoV polymerase complex, but not excised by the viral 3’-5’ ExoN activity
  3. understand in structural terms how these complex work, and 4) comparatively position these mechanisms in the viral polymerase world.

Methods used: biochemistry, enzymology, molecular biology, basic structural/biophysical methods.

The Network
This PhD position is part of the European training network ANTIVIRALS ( The candidate will benefit from the ANTIVIRALS network, which includes regular (scientific) network meetings and training in research methodology and complementary skills. This research project offers unique opportunities for establishing a broad and international scientific network with partners from the academic and industrial sector. The research project is performed in close collaboration with and partly at the premises of other institutions of the ANTIVIRALS network.

Host institute
The Structural Virology laboratory of the Architecture et Fonction des Macromolécules Biologiques AFMB is affiliated to the French CNRS and the Aix-Marseille Université (AMU). It is dedicated to structural biology, enzymology, and screening with a special emphasis on emerging viruses and Coronavirus in particular ( More precisely, the group aims at studying

  1. Viral replicases: Structure Mechanism & Drug Design;
  2. Structural Disorder and Molecular Recognition;
  3. Proteins from Emergent Viruses and Parasitology; and
  4. Antiviral Medicinal Chemistry.

Therefore, the group has developed expertise and methodologies state-of-the-art enzymology, biophysics and crystallography, molecular biology and reverse genetics, replicon studies, RNA biochemistry. The team has access to the state-of the-art facilities: X-ray crystallography, nuclear magnetic resonance (NMR), small-angle X-ray scattering (SAXS), and spectroscopic methods (CD, FTIR, fluorimetry). Furthermore, B. Canard’s group will benefit of the operating structural proteomics platform "from gene to structure", which includes parallel and robotized cloning, expression, purification and crystallization steps of targets of interest. AFMB has been among leaders in Europe for robotized crystallization and the use of nanodrops.

Research of the ESR will be embedded in the Graduate School of AMU, facilitating collaborations with other researchers involved in Infectious diseases and Microbiology in the broad Marseille area.

Candidate found. Vacancy is closed.