The impact of picornavirus and coronavirus infection on cellular metabolism: How viruses navigate the cellular maze of metabolic and signaling pathways

Abstract

Inside every cell lies a maze of metabolic and signaling pathways that coordinate essential processes. During viral infections, these pathways are often modified, either as part of viral strategies to reshape the cellular environment or due to host antiviral responses. How do viruses, particularly picornaviruses and coronaviruses, navigate this cellular maze? To address this, we investigated the impact of picornavirus and coronavirus infection on cellular metabolism as well as the impact of picornavirus infection on cellular signaling. To study the metabolic changes during picornavirus and coronavirus infection we used stable isotope tracing approaches. By tracing the fate of nutrients with stable isotopic atoms (tracers), we can analyze both the total metabolite abundance of metabolites as well as metabolic pathway activity. Picornaviruses and coronaviruses belong to two different viral families, each capable of infecting a broad range of hosts and causing diverse diseases. Well-known human picornaviruses include poliovirus, the cause of poliomyelitis, and enterovirus A71 (EV-A71), the cause of hand-foot-and-mouth disease that is associated with acute flaccid paralysis. Foot-and-mouth disease virus (FMDV) and encephalomyocarditis virus (EMCV) are picornaviruses important for animal health causing foot-and-mouth disease (FMDV) and myocarditis and encephalitis (EMCV). Coronaviruses typically cause respiratory or gastrointestinal illnesses. While most coronaviruses cause mild symptoms, some are linked to severe disease and high mortality in both humans (e.g., severe acute respiratory syndrome coronavirus [SARS-CoV] and SARS-CoV-2) and animals (e.g., transmissible gastroenteritis virus [TGEV] and infectious bronchitis virus [IBV]). Due to their ability to cross species barriers, coronaviruses can have great clinical and socio-economic impact on our society. In this thesis we show that picornaviruses and coronaviruses profoundly alter cellular metabolism. Generally, the levels of purine and pyrimidine metabolites increase during infection through an increase of RNA degradation and nucleotide recycling in the case of picornavirus infection and an increase in RNA degradation, nucleotide recycling and de novo nucleotide synthesis in the case of coronavirus infection. Additionally, we reveal that the viral proteins 2Apro of CVB3 and L of EMCV suppress de novo nucleotide synthesis during infection. We propose that the increase in RNA degradation, next to nucleotide salvage and de novo nucleotide synthesis, is important for the supply of nucleotides for viral replication. We also show that coronaviruses rewire glycolysis and the pentose phosphate pathway (PPP) during infection, which is, at least in part, caused by bystander cells. The rewiring of glycolysis and the PPP during coronavirus infection likely contributes to counteracting oxidative stress and/or supports reductive biosynthesis processes such as de novo lipogenesis and cholesterol synthesis. Additionally, this thesis provides a comprehensive overview of the activation and inhibition of kinases during picornavirus infection. Using targeted phosphoproteomics, we show that picornavirus infection leads to the activation of mitogen-activated protein kinase (MAPK) pathways and the DNA damage response (DDR), while simultaneously inhibiting kinases regulating the cell cycle. Our findings underscore the intricate interplay between viral infection and host cellular metabolic and signalling networks, offering valuable insights into virus-host interactions and potential therapeutic targets.