PNNL

Wherever bacteria are found, so are bacteriophages, a class of viruses that infect and replicate within bacteria. After infecting a bacterial cell, these viruses completely take over the internal cellular machinery and convert it into a virus-producing factory. To accomplish this takeover, viruses carry metabolic genes not directly needed for their replication, known as auxiliary metabolic genes (AMGs). The wholesale reprogramming of bacteria via viral AMG activation can be thought of as viral hijacking, but questions remain about exactly how the process operates and the overall metabolic outcome to bacterial hosts.

Research published in Science Advances and led by Pacific Northwest National Laboratory (PNNL) combined genome-scale modeling with model system experiments to understand how viral hijacking via AMGs affects cellular metabolism. They found that the virus needs to hijack just 17 targeted reactions—out of almost 1,000—to trigger a cascade that dramatically changes over 30 percent of the host cell’s metabolic network. 

“We’re trying to accurately predict how viruses hijack host cells,” said Song Feng, co-lead investigator of this study. “Historically, researchers focused on just the functions of viral genes. That approach ignores the large-scale cascading effects that occur within a cell after viral infection.”

For the modeling work, the team added viral AMGs, which redirect a host’s metabolism, and a custom representation of the virus replication into genome-scale models of the cellular host’s metabolism. This is the first time that a computational study has integrated the expression of AMGs with the explicit metabolic demands of phage assembly, developing a robust picture of hijacking behavior. 

“We were able to sort the genetic targets of the viral hijackers into two classes: ‘phage-aligned’ and ‘phage-antialigned,’” said Ruonan Wu, co-lead investigator of this study. “The phage-aligned genes directly affect the reactions and host metabolism to ramp up viral production, while the phage-antialigned genes cause large-scale metabolic disruptions in the host cell but do not individually alter the growth balance between the virus and host.”

These AMGs don’t operate in isolation, existing within a complex overall metabolic system. They exhibit interdependent behaviors, positive and negative, while regulating the host cell metabolism. This is particularly crucial for the phage-antialigned genes, which were found to affect the viral product only when combined with other AMGs.

“This research was led by some exceptionally talented and creative early career staff,” said Margaret Cheung, a PNNL computational scientist and the principal investigator of the Northwest Biopreparedness Research Virtual Environment (NW-BRaVE) project. “Delivering results required asking questions and looking at the science in different ways.”

The simulations focused on the important marine cyanophage P-HM2. The PNNL team, in partnership with collaborators from the University of Illinois at Urbana-Champaign, experimentally validated the simulation predictions by synthetically inserting P-HM2 AMGs into mutant cyanobacteria. 

Using knowledge from the simulations, the team was able to specifically look at how the environment affects the metabolic hijacking. One key example is the viral cp12 gene, which causes severe metabolic issues for the host in an environment with sufficient nutrients. However, when nitrogen is limited, so is the impact of cp12.

These insights connecting environmental conditions to viral strategies offer a framework for predicting how viruses reshape cellular metabolism at a large scale, with implications for nutrient cycling and biotechnology. The team is looking at how their work can translate to biotechnological innovations, ranging from better industrial bioproduction to targeted phage therapies to cure diseases.

The work was primarily supported through the U.S. Department of Energy BRaVE Initiative. “NW-BRaVE is a multi-institutional team of researchers led by PNNL,” said Cheung. “Our objective is to create a powerful and user-friendly integrative platform in a virtual environment to reveal the fundamental principles of how molecular interactions drive pathogen–host relationships and host shifts.”

In addition to Cheung, Feng, and Wu, the PNNL team included Jordan Rozum (co-first author), Willian Sineath (co-first author), Pavlo Bohutskyi, Doo Nam Kim, Connah Johnson, James Evans, David Pollock, and Wei-Jun Qian. The team also included Angad Mehta and Jordan Quenneville of the University of Illinois at Urbana-Champaign. NW-BRaVE is funded by the U.S. Department of Energy, Office of Science, Biological and Environmental Research program. The work was also supported by the U.S. Department of Energy, Office of Science, Office of Workforce Development for Teachers and Scientists under the Science Undergraduate Laboratory Internships Program and an Environmental Molecular Sciences Laboratory user project.