Giant Viruses Spew Their DNA Through A Stargate

September 30, 2020

Giant viruses, about 10 times the size of a typical cold virus, infiltrate cells and inject their DNA through a special portal called a “stargate. “Now, detailed new images have revealed what conditions prompt this stargate to open and drive viral infection.

Viruses, giant or otherwise, lack the machinery needed to replicate their DNA; microbes are essentially just a ring of genetic material, hidden inside an envelope called a capsid. In order to survive, the virus must infiltrate inside the host cell, hijack the machinery inside, and build what is called a virus factory to produce new viruses. Giant viruses have a special entry point to do this job: the stargate.

Shaped like an open starfish with five legs, the stargate sits on the surface of the virus and remains sealed for most of its life cycle. But once inside the host cell, each leg of the stargate “unravels,” allowing the virus’ genetic material to slip through the resulting hole, said senior author Kristen Parent, an associate professor of biochemistry and molecular biology at Michigan State University.The new study, published May 8 in the journal Cell, shows that the stargate opens under acidic, salty and hot environmental conditions.

Parent told Live Science that when the stargate opens, other proteins slip out along with the viral DNA.” We can determine which [proteins] are actually coming out of the capsule during that opening event,” she said.Parent and her team plan to explore how these proteins work and what role they play in giant viral infections to better understand these large and mysterious microbes.

Huge and mysterious
According to the journal Science, scientists have been discovering giant viruses for a relatively short time; the first study describing a giant virus was published in 2003.

In that report, Parent said, the giant microbes were isolated from water samples collected in the early 1990s, before scientists were unable to scrutinize the genetic code of the virus. At the time of the collection, researchers believed that because of the microbes’ large size, they must be bacteria. Giant viruses are more than 0.00001 inches (300 nanometers) in diameter, or about 10 times larger than your average rhinovirus, and according to one statement, they can cause the common cold.

Mistaken for big bacteria, megaviruses were essentially “discovered a decade ago [that scientists] know what they’re looking at,” Parent said. Once the technology became available, researchers dug up samples and found that the large microbes lacked ribosomal RNA – the key molecule that allows bacteria to build their own proteins and that viruses can’t do on their own.

Since their initial discovery, the giant viruses have been found in the melting permafrost of Siberia, the depths of the Antarctic ocean and highly alkaline soda lakes, as well as in less exotic environments, said Chantal Abegger, director of research at the Structural and Genomic Information Laboratory at the French National Center for Scientific Research, who was not involved in the study. The viruses have mostly been found to infect amoebas and phytoplankton, but laboratory studies have shown that they can also infect animal cells, including rodent and human cells. However, “no direct link has been established between GV and human disease,” the authors note.

“You can find them in a variety of environments,” Abergel said. In all likelihood, they were ignored for decades as scientists filtered out large particles from water samples in their search for smaller viruses, Abergel added. In addition to being large, the giant viruses have a number of unique features that set them apart from any smaller viruses seen before, she added.

For example, Parent and her collaborators studied several giant viruses that look like 20-sided dice, including mimivirus, Antarctica virus, Samba virus, and Tupanvirus. the structures and shells of these viruses are “very complex and have never been seen before in a virus ball.” J?natas Abrah?o, study author and associate professor of virology at the Federal University of Minas Gerais in Brazil, told Live Science in an email.Abrah?o said the stargates found on the surface of these viruses particularly fascinated scientists “due to their beauty and symmetry” and the fact that no smaller viruses contain such structures.

But until now, “how to open the stargate has remained a mystery,” he added.

Open the stargate.
Before the stargate opens, Parent says, giant viruses are “swallowed” by cells in a process called phagocytosis. While small viruses like the flu fuse their fatty membranes with the fatty membranes of the cells they infect, mega-viruses enter cells by being swallowed whole, hard shell and all.

Once inside the cell, the mega-viruses open the stargate and release their infectious “seeds,” says Abergel.” It’s an aqueous solution of proteins and salts downloaded from plasmids” or rings of viral DNA into entire structures in the cytoplasm, or the proteins and salts that surround organelles in eukaryotic cells. This process initiates the infection, she said.

In previous studies, Parent said, researchers have captured snippets of the process by slicing infected cells into thin slices and studying what can be found inside. But unless someone happens to capture a “one-in-a-million” snapshot of a stargate opening, the slicing technique makes it difficult to distinguish one stage of infection from the next, she added.

To overcome this obstacle, Parent and Jason Schrad, a graduate student in her lab, devised a strategy to trigger giant viral infections outside the cell and to image each step of the process.

After isolating the virus, the team subjected each sample to different chemical and environmental treatments in an attempt to mimic the conditions inside the actual cell that could trigger infection. For example, after being engulfed by the cell, the virus sits in a membrane-like bubble called a vacuole, which tends to be very acidic (low pH). The team then placed the treated virus under a cryo-electron microscope (EM) microscope, which passes a beam of negatively charged particles through the sample to capture atomic-resolution images. They also used a scanning electron microscope to scan the sample and take detailed images of the virus surface.

The team found that three conditions reliably unlocked the stargate: low pH, high salt concentration, and high temperature, up to 212 degrees Fahrenheit (100 degrees Celsius).

The authors note that low pH or high salt, in isolation, “cracked” the stargate, but did not fully open the structure. The addition of extreme heat opens the gateway more, but is unlikely to find the boiling temperature in real cells, Parent said. More likely, the high temperature mimics the effects of other things that happen “in the context of the host,” such as the presence of specific enzymes, she said.

Under many conditions, giant viruses resist opening their stargates, “however, if you have the right key, they will open very nicely,” similar to a tough seed breaking open with water, Abergel said. In her lab’s previous work, Abergel predicted that low pH and high salt concentrations could cause the stargates to open. She said of the Cell study, “It’s great to see this model being demonstrated experimentally.”

There are more mysteries to solve.
After coaxing the stargate open, the team went on to study the proteins that slip out of viruses along with their genetic material. Focusing specifically on the Samba and Tuban viruses, they used a technique called mass spectrometry to infer the structure of different proteins.

“The shapes of viral proteins and the way they work tend to be conserved in very distantly related [viruses],” says Parent. In future studies, the authors aim to determine how these giant viral proteins function, in part by “chopping up the protein sequences [into small pieces]” and comparing their structures to other known proteins.

“The proteins released during [mega-viral] uncoating may be related to the initial steps of infection, including shutting down the host response and virus factory assembly,” says Abrah?o.” However, many of the viral proteins released from capsids are unknown, and their functions have yet to be investigated.”

The 20 faceted viruses included in the study represent just one class of megaviruses, but the same approach could be used to study many other species, “whose genomes and particles have never been described,” Abrah?o said. Megaviruses contain genes and proteins that “do not resemble anything in the cellular world,” even with other viruses, Abergel added. Future research could shed light on when and how these viruses first evolved, and why they differ so dramatically from more familiar forms of life.