Biology subjects

Bunel, L.

Publications and source records attributed to Bunel, L..

3 recordsLinked to original sources

bioRxiv2026

SARS-CoV-2 nucleocapsid protein engages with viral RNA and ERGIC lipids to drive viral core assembly

Severe acute respiratory syndrome coronavirus 2 assembles at the ER-Golgi intermediate compartment (ERGIC), yet the molecular basis of nucleocapsid (N) protein interactions with host membranes remains unclear. Using in vitro reconstituted lipid membranes and viral RNA- N complexes, we show that full-length N binds phosphatidylinositol (PI)- and phosphatidylserine (PS)-containing membranes and induces lipid clustering, an effect amplified by viral RNA and ERGIC-like membrane lipid composition. The isolated N-terminal domain lacks this activity, whereas the C-terminal domain retains membrane-associated multimerization. Although, lipid bilayers promote co-clustering of N and PI lipids, facilitating ribonucleoprotein (RNP) assembly, even on simple membranes. Importantly, ERGIC- mimicking membranes enhances this co-clustering further stabilizing RNPs of dimensions matching the viral core. In cells, viral RNA enhances N clustering without altering particle production. These findings reveal cooperative interactions between N, viral RNA, and ERGIC lipids as key drivers of lipid-dependent viral core formation, providing a mechanistic framework for the early steps of viral assembly.

biophysics↗

bioRxiv2025

Functional selection in a population of synthetic cells with a minimal metabolism

Various synthetic microcompartment systems have been developed to mimic key features of living cells. Here, we focus on artificial cells that capture their capacity to serve as vessels for Darwinian evolution. We assemble micro-compartmentalized In Vitro Transcription-Translation-Replication systems containing a minimal genome, a basic metabolic pathway, a reconstituted protein expression machinery, and a simple DNA replication module, wired in a positive feedback loop. The minimal genome encodes the enzyme deoxyribonucleoside kinase (DNK) whose expression, and then metabolic activity, is required for the genomes replication. We show that these compartments act as minimal Darwinian elements by filtering out non-functional genotypes. We track individual replicators from a library of 42 genetic variants to reveal the systems dynamics at both the population and the single replicator levels. At the population level, we extract the fitness function, which links a genomes metabolic efficiency to its selective success, considering co-encapsulation and hitch-hiking effects. At the individual replicator level, we observe a bimodal distribution of replication yields and propose a mixed model with an inter-droplet heterogeneity with presence or absence of a metabolic feedback loop on the replicator. In addition, we leverage this autonomous self-selection loop to generate a high-resolution mutational map of the DNK enzyme.

synthetic biology↗

bioRxiv2023

A model for collagen secretion by intercompartmental continuities

Newly synthesized secretory proteins are exported from endoplasmic reticulum (ER) at specialized subcompartments called exit sites (ERES). Cargoes like procollagen are too large for export by the standard COPII-coated vesicle of 60 nm average diameter. We have previously suggested that procollagen is transported from the ER to the next secretory organelle, the ERGIC, in TANGO1-dependent inter-organelle tunnels. Here, we show that intrinsically disordered domains of TANGO1 in the ER lumen generate an entropic contraction that pulls procollagen towards the ERES. Molecular gradients of pH and HSP47 between the ER and ERGIC generate a force in the range of tens of femtoNewtons (fN), which is sufficient to propel procollagen from the ER at a speed of [~]1 nm.s-1. This calculated speed and the quantities of collagen secreted are similar to its observed physiological secretion rate in fibroblasts, consistent with the proposal that ER export is the rate limiting step for procollagen secretion. Our theoretical model explains how cells can utilize molecular gradients to export procollagens at a rate commensurate with physiological needs. Significance StatementProcollagen cannot be exported from the endoplasmic reticulum (ER) by standard COPII-coated vesicle of 60 nm average diameter. We have previously suggested that collagen is transported from the ER to the next secretory organelle, the ERGIC, in TANGO1-dependent inter-organelle tunnels. ER and ERGIC differ in molecular composition including their pH and protein composition. We propose a mechanical/entropic ratchet model whereby molecular gradients of pH and the collagen chaperone HSP47, provide the energy to propel procollagen from the ER at a speed that matches the physiological rate of collagen secretion.

biophysics↗