Hepatitis C virus (HCV) has the unique characteristic of forming lipo-viro-particles (LVPs), which are lipid-rich virions containing both the viral components and host apolipoproteins such as ApoB and Show more
Hepatitis C virus (HCV) has the unique characteristic of forming lipo-viro-particles (LVPs), which are lipid-rich virions containing both the viral components and host apolipoproteins such as ApoB and E. This unique composition gives to LVPs a low buoyant density, facilitates their entry into the hepatocyte, and is a hallmark of highly-infectious HCV particles. Although recent studies have shown that inhibiting NAD biosynthesis can both disrupt central carbon metabolism and thereby interfere with the replication of hepatotropic viruses such as dengue virus (DENV) and hepatitis B virus (HBV), the impact of nicotinamide biosynthesis inhibition on HCV replication and LVP formation has not yet been explored. We therefore investigated the dependance of HCV on NAD(H) biosynthesis in Huh7 cells by using the antimetabolite 6-Aminonicotinamide (6-AN) or by specifically inhibiting NAMPT, a key enzyme in the nicotinamide salvage pathway. The impact on cellular metabolism was assessed by LC-MS/MS to quantify metabolites, by confocal microscopy to analyze lipid droplets and by ELISA for ApoB/E secretion. Glycolytic activity and mitochondrial respiration were evaluated by real-time measurement of extracellular acidification rate (ECAR) and oxygen consumption rate (OCR), respectively. Consequences on viral replication were analyzed using both a subgenomic replicon (strain JFH1) and the full-length infectious virus (strain Jc1). The effect of 6-AN on the formation of double-membrane vesicles (DMVs) where the virus replicates was determined transmission electron microscopy. Finally, the secretion and specific infectivity of virions were analyzed by RT-qPCR and titration technics, either before or after separation by density-gradient centrifugation to focus on LVPs. Pharmacological inhibition of NAD(H) biosynthesis in Huh7 cells impaired HCV replication, the formation of DMVs and the production of infectious LVPs. Mechanistically, 6-AN drastically inhibited glycolysis but increased oxidative phosphorylation as compensatory mechanism. This metabolic reprogramming was associated with decreased intracellular levels of triglycerides, smaller lipid droplets and reduced secretion of Apo B and E, which altogether could explain the impact of 6-AN on HCV replication and the production of LVPs. Inhibiting NAD(H) biosynthesis disrupts central carbon metabolism, reduces intracellular triglycerides and blocks ApoB ⁺ -lipoprotein secretion-a pathway essential for HCV replication and LVP production. These results reveal, for the first time, that HCV life cycle is critically dependent on NAD(H) metabolism, reinforcing the interest of this pathway as a potential therapeutic target against hepatotropic viruses. Show less
Recent years have seen a dramatic improvement in protein-design methodology. Nevertheless, most methods demand expert intervention, limiting their widespread adoption. By contrast, the PROSS algorithm Show more
Recent years have seen a dramatic improvement in protein-design methodology. Nevertheless, most methods demand expert intervention, limiting their widespread adoption. By contrast, the PROSS algorithm for improving protein stability and heterologous expression levels has been successfully applied to a range of challenging enzymes and binding proteins. Here, we benchmark the application of PROSS as a stand-alone tool for protein scientists with no or limited experience in modeling. Twelve laboratories from the Protein Production and Purification Partnership in Europe (P4EU) challenged the PROSS algorithm with 14 unrelated protein targets without support from the PROSS developers. For each target, up to six designs were evaluated for expression levels and in some cases, for thermal stability and activity. In nine targets, designs exhibited increased heterologous expression levels either in prokaryotic and/or eukaryotic expression systems under experimental conditions that were tailored for each target protein. Furthermore, we observed increased thermal stability in nine of ten tested targets. In two prime examples, the human Stem Cell Factor (hSCF) and human Cadherin-Like Domain (CLD12) from the RET receptor, the wild type proteins were not expressible as soluble proteins in E. coli, yet the PROSS designs exhibited high expression levels in E. coli and HEK293 cells, respectively, and improved thermal stability. We conclude that PROSS may improve stability and expressibility in diverse cases, and that improvement typically requires target-specific expression conditions. This study demonstrates the strengths of community-wide efforts to probe the generality of new methods and recommends areas for future research to advance practically useful algorithms for protein science. Show less