Map of protein modification sites may reveal antimicrobial targets

Using a new approach, researchers at the University of Iowa Carver College of Medicine and the VIB-UGent Center for Medical Biotechnology in Belgium, are investigating a poorly understood mechanism used by the immune system to fight infections.

The mechanism involves a small protein called ISG15, which “tags” other proteins and modifies their function. Previous work suggests that ISG15 has anti-viral activity, but unravelling the details of its function in immune defense has been hindered by the fact that the identity of the modified proteins and their exact sites of modification are still unknown.

In the new study, published Nov. 26 in Nature Communications, the team led by Lilliana Radoshevich, PhD, assistant professor of microbiology and immunology at the UI Carver College of Medicine, and Francis Impens, PhD, head of the VIB proteomics core at VIB-UGent Center for Medical Biotechnology, combined their expertise to discover almost 1,000 sites on over 400 proteins that are tagged with ISG15 during infection. This comprehensive map of ISG15 sites could pave the way to understanding the consequences of ISG15 modification on protein fate and function.

Small proteins can tag others to control the target protein’s activity, localization and function. One of the best-known protein tags is called ubiquitin, which primarily targets proteins for degradation, in addition to a variety of other functions. 

Unlike ubiquitin, which is present at all times, ISG15 is only expressed when cells are under stress such as a viral or bacterial infection. So, the researchers infected mice with Listeria monocytogenes, a food-borne bacterial pathogen that causes sepsis, meningitis, and fetal infection in pregnant women, and then analyzed the animals’ livers using technology developed to identify ubiquitin modification sites.

The comprehensive list of ISG15-tagged proteins revealed new links between ISG15, cellular metabolism, and autophagy‑a cellular process that leads to the destruction of damaged cells or pathogens to generate new sources of energy and promote cell survival. Radoshevich notes that abnormal autophagy has also been implicated in several neurodegenerative diseases, including Parkinson’s disease and Alzheimer’s.

“We found that ISG15 targets numerous enzymes involved in metabolic processes, but also that it targets key regulators of autophagy,” Radoshevich says. “Our finding that ISG15 modulates this process is most exciting.” 

The researchers plan to use their approach to investigate ISG15 targets during infection with other pathogens such as Influenza virus or Coxsackie virus. These studies may reveal antimicrobial pathways in the immune system that might be exploited to design new drugs. 

In addition to Radoshevich and Impens, the research team also included third-year University of Iowa graduate Student, Yifeng Zhang, from the Microbiology Program, University of Gent graduate student Fabien Thery, Nicholas Wu from The Scripps Research Institute and colleagues in Paris, France, and Berlin, Germany.