Postdoctoral position: Mimicking the intracellular milieu to understand virus self-assembly
A two-year postdoctoral fellowship is available in the field of physical virology at the Université Paris-Saclay (Orsay, France). This research project is conducted in collaboration with the Institute of Molecular Microbiology and Structural Biochemistry (Lyon, France), the Montpellier Institute for Research in Infectiology (Montpellier, France), the University of California, Los Angeles (Los Angeles, CA), and the University of California, Riverside (Riverside, CA). Applications from candidates with a PhD in biological physics, physical chemistry, or structural biology are welcome.
Background. Most viruses have as their genome – not double-standed (ds)DNA, as is the case with all other evolving organisms, but rather – single-stranded (ss)RNA. Further, because ssRNA is much more compact and compressible than dsDNA, it is possible to make ssRNA-genome virus particles from their purified components, ssRNA and capsid protein, by simply mixing these components in physiological buffer solution. Each infectious particle consists of a single RNA molecule inside a shell comprised of hundreds of copies of the capsid protein. These remarkable facts have facilitated a large number of experimental and theoretical investigations of the underlying co-assembly process – the self-assembly of perfectly-ordered/icosahedrally-symmetric nucleocapsids. And it is widely believed that this “test-tube”/in vitro phenomenon mimics the formation of a new generation of virus particles in their host cell, following the replication of their ssRNA genome and the synthesis of a hundreds-of-times-larger number of capsid proteins. But, in fact, there is to date essentially no experimental or theoretical program that sets out to bridge the gap between the knowledge bases acquired from in vitro studies of virus self-assembly on the one hand and intracellular viral replication on the other. In the present project, we propose a first set of systematic steps towards connecting these two sets of phenomena.
Project description. In particular, we argue that the difference between in vitro and intracellular (cytoplasmic) self-assembly of virus particles from their RNA and capsid protein is twofold: (1) in cytoplasm these basic components are embedded in a concentrated solution of proteins and nucleic acids that is highly viscous and whose osmotic effects alter the conformations of and interactions between the viral RNA and capsid proteins; and (2) in the cellular context, the capsid proteins are being actively synthesized, i.e., through ATP consumption, by the ribosomal machinery so that a nearly-constant influx of capsid proteins drives the virus self-assembly process towards a nonequilibrium state. To connect the in vitro and cellular contexts, we propose to extend our earlier measurements of virus self-assembly from purified RNA and capsid protein components by carrying these reactions in the controlled presence of calibrated osmolytes and by synthesizing capsid protein in cytoplasmic extracts where messenger (m)RNA is translated into capsid protein which in turn packages it into nucleocapsids. These processes will be investigated and quantified by a mix of state-of-the-art: experimental techniques including solid-state NMR, time-resolved synchrotron X-ray scattering, cryotransmission electron and super-resolution fluorescence microscopies; and analytical theory and coarse-grained computer simulations. All of this work will be carried out for a mammalian virus – Hepatitis B virus (HBV), which has a DNA genome but whose genetic information is packaged in the cytoplasm in mRNA form well characterized by in vitro studies – in order to provide for the first time a general foundation for and understanding of virus self-assembly in cellular environment.
Contact: Guillaume Tresset
Availability: September 2026
Duration: 24 months
Monthly gross salary: €3.5k – €4.5k based on experience
Stage L3/M1: Objets biologiques par microscopie électronique en phase liquide
La microscopie électronique en phase liquide est une technique très prometteuse qui nécessite encore beaucoup de développements. Elle permet en principe d’obtenir des images avec des résolutions nanométriques, dans un environnement aqueux natif aux objets biologiques. Les processus dynamiques sont a priori accessibles, ce que n’autorise pas la microscopie électronique conventionnelle. Le stage consistera à poursuivre le développement méthodologique entrepris dans notre équipe. Les paramètres d’observations (temps d’exposition, courant du faisceau), les traitements numériques d’images, la préparation des échantillons (volume, solvant, force ionique) seront à optimiser. Les objets seront des virus non infectieux, ou des condensats biomoléculaires.
Durée: 2 mois
Contacts: Guillaume Tresset / Amélie Leforestier
Stage L3/M1: Modélisation de l’auto-assemblage d’une capside du virus de l’hépatite B par apprentissage automatique
La capside du virus de l’hépatite B est la coque protéique qui entoure et protège son matériel génétique. D’environ 35 nm de diamètre, elle est produite dans la cellule infectée par auto-assemblage de 240 protéines identiques. En utilisant la diffusion des rayons X aux petits angles avec une source synchrotron, nous avons collecté des diffractogrammes retraçant la cinétique dans l’espace réciproque. L’objectif du stage est de mettre en place un algorithme d’apprentissage automatique sous Python afin d’identifier la morphologie des objets en cours d’assemblage dans l’espace direct, et ce, à partir d’une base de données théorique à construire.
Durée: 2 mois
Contacts: Guillaume Tresset