Human RNA triggers a transformation in a vital protein from Ebola virus

April 29, 2021
The way Ebola responds to human RNA may lead to a way to defeat it. (CDC via AP/Frederick Murphy)

The way Ebola responds to human RNA may lead to a way to defeat it. (CDC via AP/Frederick Murphy)

A key protein produced by the Ebola virus transforms into different shapes depending on whether human genetic material is nearby, suggesting a potential target for drugs to fight the deadly pathogen.

Scientists identified certain sequences of messenger RNA — single-stranded molecules that carry protein-building instructions — that triggered the protein to change from a butterfly-like form into a ring. The team reported the findings April 13 in Cell Reports.

Ebola virus disease is rare but can lead to severe bleeding, organ failure and death. Only two treatments for Ebola have been granted approval by the U.S. Food and Drug Administration, both in late 2020, although other potential treatments are in development; the agency approved the first vaccine against Ebola in late 2019. There are two ongoing Ebola outbreaks in Guinea and the Democratic Republic of the Congo.

To make more copies of themselves, viruses must hijack the cellular machinery of their hosts. But for viruses that use RNA as their genetic material, this replication process is rife with errors.

The virus that causes Ebola is particularly incapable of proofreading to make sure its genetic material is copied correctly, says Erica Ollmann Saphire, a professor at the La Jolla Institute for Immunology, in San Diego, and last author of the study. Most of the mutations this leads to are detrimental to the virus. So it's in the virus's interest to keep its genome small, leading to fewer opportunities for mistakes; the Ebola virus has just seven genes.

"They encode just a handful of tools, and so that's the central question: How do they do so much with so little?" Saphire said. "We know there are at least 70 different things that happen in the viral life cycle for Ebola."

The proteins these genes code for must be able to play multiple roles, behaving more like a Swiss Army knife than a Phillips-head screwdriver. One particular protein, known as VP40, has captivated Saphire and her team.

"What's really cool about this one is how it unfolds and refolds to be different shapes for different tools at different times," she said.

She likens it to a piece of origami paper that can fold into a frog or a sailboat, or to a ball of yarn.

"The information that's encoded in the polypeptide chain would be like yarn that could knit into a sweater for you to wear in the morning, and unknit and reknit into a parachute when you have to leap out of a plane, and then unknit and reknit into pajamas in the evening," Saphire said.

Previously, she and her colleagues found that VP40 can fold itself into several shapes. One is a two-molecule, butterfly-shaped form, called a dimer, that helps build "the shell and shape of the virus," Saphire said. Inside infected cells, the protein can also build an eight-molecule, wreath-shaped form, called an octamer, that can bind to RNA. 

This shape has "some kind of controlling function on how the virus executes its life cycle inside the cell," Saphire said. 

She and her colleagues wanted to know which bits of RNA the protein would affix to in mammalian cells.

"What we were missing would be how and why it would change from one to the other," Saphire added. "As the protein was first born, did it irreversibly fall down one folding pathway and destiny or another?"

She and her team exposed VP40 to cultured human cells and found that it latched onto human rather than viral RNA. Next, the team presented the protein with thousands of different snippets of human genetic material and concluded that VP40's transformation is triggered by mRNA sequences rich in the building blocks guanine and adenine.

Intriguingly, the sequences came from parts of the mRNA strands that didn't code for proteins; these untranslated regions help regulate how the instructions contained in the protein-coding parts of the mRNA are carried out. This indicated that VP40 didn't require a specific gene or protein to work its transformation. 

However, the team did notice that some sequences that were "particularly favored" by VP40 came from genes that code for proteins released in response to stress, including one called HSPA1B, said Hal Wasserman, a postdoctoral fellow at the La Jolla Institute for Immunology and co-author author of the study.

"We theorize that Ebola infection causes the cell to produce a large amount of HSPA1B and similar proteins, and that Ebola then takes advantage of the mRNA for its own purposes," Wasserman said.

The researchers observed that these mRNA sequences could trigger the butterfly form of VP40 to refold into the octamer wreath. 

"It was identical to the protein that was 'born' as octamer," Saphire said. "So this protein is like multiple computer programs all at once, and by sensing the presence and absence of things in the infected cell environment, it knows which one of those programs it needs to execute."

To complete its life cycle, the Ebola virus relies on its ability to make VP40 play multiple roles. This indicates that a drug that targets VP40 could wreak havoc on Ebola by knocking out several essential functions at once. What's more, the virus may be unable to mutate and "escape" the drug because it can't tolerate much change to this crucial protein.

"It tells you that that's a key molecule to attack, and it might help you home in on what the different sites are that you might use to attack it," Saphire said. "We'd like to next learn [more about] what the functions are that it achieves by transforming and what other viral proteins do this."

The study, "Cellular mRNA triggers structural transformation of Ebola virus matrix protein VP40 to its essential regulatory form," published April 13 in Cell Reports, was authored by Sara Landeras-Bueno, Hal Wasserman, Zhe Li Salie and Erica Ollmann Saphire, La Jolla Institute for Immunology; Glenn Oliveira and Kristian Andersen, Scripps Research Institute; and Zachary L. VanAernum, Florian Busch and Vicki H. Wysocki, The Ohio State University.

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