Flu virus key machine: First complete view of structure revealed

The complete structure allows researchers to understand how the polymerase uses host cell RNA (red) to kick-start the production of viral messenger RNA. Credit: © EMBL/P.Riedinger

Scientists looking to understand -- and potentially thwart -- the influenza virus now have a much more encompassing view, thanks to the first complete structure of one of the flu virus' key machines. The structure, obtained by scientists at EMBL Grenoble, allows researchers to finally understand how the machine works as a whole, and could prove instrumental in designing new drugs to treat serious flu infections and combat flu pandemics.

If you planned to sabotage a factory, a recon trip through the premises would probably be much more useful than just peeping in at the windows. Scientists looking to understand -- and potentially thwart -- the influenza virus have now gone from a similar window-based view to the full factory tour, thanks to the first complete structure of one of the flu virus' key machines. The structure, obtained by scientists at the European Molecular Biology Laboratory (EMBL) in Grenoble, France, allows researchers to finally understand how the machine works as a whole. Published in two papers in Nature, the work could prove instrumental in designing new drugs to treat serious flu infections and combat flu pandemics.

The machine in question, the influenza virus polymerase, carries out two vital tasks for the virus. It makes copies of the virus' genetic material -- the viral RNA -- to package into new viruses that can infect other cells; and it reads out the instructions in that genetic material to make viral messenger RNA, which directs the infected cell to produce the proteins the virus needs. Scientists -- including Cusack and collaborators -- had been able to determine the structure of several parts of the polymerase in the past. But how those parts came together to function as a whole, and how viral RNA being fed in to the polymerase could be treated in two different ways remained a mystery.

"The flu polymerase was discovered 40 years ago, so there are hundreds of papers out there trying to fathom how it works. But only now that we have the complete structure can we really begin to understand it," says Stephen Cusack, head of EMBL Grenoble, who led the work.

Using X-ray crystallography, performed at the European Synchrotron Radiation Facility (ESRF) in Grenoble, Cusack and colleagues were able to determine the atomic structure of the whole polymerase from two strains of influenza: influenza B, one of the strains that cause seasonal flu in humans, but which evolves slowly and therefore isn't considered a pandemic threat; and the strain of influenza A -- the fast-evolving strain that affects humans, birds and other animals and can cause pandemics -- that infects bats.

"The high-intensity X-ray beamlines at the ESRF, equipped with state-of-the-art Dectris detectors, were crucial for getting high quality crystallographic data from the weakly diffracting and radiation sensitive crystals of the large polymerase complex," says Cusack. "We couldn't have got the data at such a good resolution without them."

The structures reveal how the polymerase specifically recognises and binds to the viral RNA, rather than just any available RNA, and how that binding activates the machine. They also show that the three component proteins that make up the polymerase are very intertwined, which explains why it has been very difficult to piece together how this machine works based on structures of individual parts.

Although the structures of both viruses' polymerases were very similar, the scientists found one key difference, which showed that one part of the machine can swivel around to a large degree. That ability to swivel explains exactly how the polymerase uses host cell RNA to kick-start the production of viral proteins. The swivelling component takes the necessary piece of host cell RNA and directs it into a slot leading to the machine's heart, where it triggers the production of viral messenger RNA.

Now that they know exactly where each atom fits in this key viral machine, researchers aiming to design drugs to stop influenza in its tracks have a much wider range of potential targets at their disposal -- like would-be saboteurs who gain access to the whole production plant instead of just sneaking looks through the windows. And because this is such a fundamental piece of the viral machinery, not only are the versions in the different influenza strains very similar to each other, but they also hold many similarities to their counterparts in related viruses such as lassa, hanta, rabies or ebola.

The EMBL scientists aim to explore the new insights this structure provides for drug design, as well as continuing to try to determine the structure of the human version of influenza A, because although the bat version is close enough that it already provides remarkable insights, ultimately fine-tuning drugs for treating people would benefit from/require knowledge of the version of the virus that infects humans. And, since this viral machine has to be flexible and change shape to carry out its different tasks, Cusack and colleagues also want to get further snapshots of the polymerase in different states.

"This doesn't mean we now have all the answers," says Cusack, "In fact, we have as many new questions as answers, but at least now we have a solid basis on which to probe further."

Source: European Molecular Biology Laboratory (EMBL)

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Study may help slow the spread of flu

A false color image of an influenza virus particle, or “virion.” Credit: Centers for Disease Control/Cynthia Goldsmith

An important study conducted in part at the Department of Energy's SLAC National Accelerator Laboratory may lead to new, more effective vaccines and medicines by revealing detailed information about how a flu antibody binds to a wide variety of flu viruses.

The flu virus infects millions of people each year. While for most this results in an unproductive and uncomfortable week or two, the flu also contributes to many deaths in the average flu season. And while vaccines are effective in preventing the flu, they require almost yearly reformulation to keep up with the constantly changing virus.

At SSRL and APS, a team of researchers from The Scripps Research Institute, Fujita Health University and Osaka University studied both samples of flu virus components and an anti-flu antibody. The antibody, called F045-092, was already known to neutralize the flu by connecting to the region of the flu virus that binds to host cells, so it can no longer bind to its target and cause infection.

"There are patches of the virus that are more hypervariable than others," said Peter Lee, a postdoctoral research associate at The Scripps Research Institute and first author of the paper. "But the flu always binds to host cells within the same region, and so that binding site needs to be functionally conserved. That makes it a site of vulnerability."

The team used the X-ray beams at SLAC's Stanford Synchrotron Radiation Lightsource (SSRL) and Argonne National Laboratory's Advanced Photon Source (APS), both DOE Office of Science User Facilities, to view the structure of the antibody bound to one subtype of the flu virus called H3N2. They discovered that the antibody inserts a loop into the binding site of the virus, which would otherwise attach to a receptor in a host cell. Additional experimental data showed that F045-092 binds a wide variety of strains and subtypes, including all H3 avian and human viruses from 1963 to 2011 that were tested.

This understanding of the antibody's structural details and binding modes offers new insight for future structure-based drug discovery and novel avenues for designing future vaccines.
But the only way to achieve those goals is for many groups of scientists to work together, Lee said. "Our lab is very focused on the structure of the virus and antibodies, while there are lots of other labs focused on everything from small protein design to vaccine design," he said. "Hopefully we can use this structural information and join together as one big team to tackle the flu."

Source: SLAC National Accelerator Laboratory

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Mapping bats could help stop Ebola's spread

Fruit bats (Pteropodidae) are considered the likely host of the Ebola virus. Credit: Satit Srihin

In the fight against Ebola, mapping fruit bat habitats could be one important step, says a geoinformatics researcher at Sweden's Royal Institute of Technology.

Like the Black Death that ravaged medieval Europe, the Ebola virus' progress through remote areas of West Africa is enabled by lack of understanding about the disease, including its causes and transmission.

Mapping technology however will give responders to the crisis in Africa the upper hand in stopping the spread of the deadly disease, says Skog, a researcher in geoinformatics at Sweden's KTH Royal Institute of Technology.

Skog's research has produced a method that medical professionals can use to visualise the geographical distribution of a disease over time. In his research, Skog has explored the relationship between geography and disease distribution in major epidemics of the past, including the Black Death, the Russian Flu pandemic of 1889, the Asiatic Influenza of 1957 and the swine flu. He says the historical data provides a basis for predicting the course of future epidemics and pandemics.

"My research and method can also be used to report the current state of a pandemic, or predict how extensive the spread will be. And where the disease will strike next," Skog says.

In fact, the way in which Black Death spread during the mid 14th, century bears a no small resemblance to today's Ebola epidemic, he says. Both diseases were hosted by small mammals -- black rats and fruit bats, respectively. But ultimately it was humans that enabled its spread.

"The Black Death was very much depending on total lack of knowledge regarding the etiology of the disease and how to avoid further transmission," Skog says. "That is also the case for the mainly remote locations where Ebola now is spread."

Fruit bats are believed to be the natural hosts of Ebola. These bats are among the creatures that residents of rural West Africa hunt for "bush meat." The disease is also spread by the droppings of the bat, and it is believed to have spread to other types of bush meat, as well as monkeys and pigs that are raised for slaughter.

"The local population is getting part of their nourishment from bush hunting, leading to contact with the virus that is transmitted via body fluids," Skog says, suggesting that closer study of the fruit bat could provide vital answers.

"A guess of mine is that the number of infected fruit bats is a determining factor for an Ebola outbreak," he says. "Are there any known factors that may have changed the ecosystem in favor of the bats? Are the bats affected by the virus too? Do fruit bats always carry the Ebola virus or is the virus fatal to them as well? If so the percentage of infected bats will vary over the years also depending on the immunology of the species."

There are a number of geoinformation technology options available to public health organizations that have sent field crews to respond to the crisis. These, Skog says, including equipping field workers with hand-held GPS devices that feed a central database with data and findings regarding locations of bodies, possible infections and diagnosed cases personnel.

"The data can easily be centrally monitored and used for decisions and policies to mitigate the spread," he says. "Using satellite imagery, population centers can be localized. Collected disease data can also be compared and analysed with environmental and climatologic data to support other efforts to control the spread."

For instance, assuming that fruit bats are the reservoir for the ebola virus, Skog says it would be of interest to find out if the first detected cases in an outbreak are located in or close to a fruit bat habitat. "If the environmental and climatologic parameters for fruit bat habitats can be defined, there is a chance these habitats could be mapped using existing map data and satellite or airborne imagery," he says.

"Then risk areas could be monitored and preventive measures could be performed by health authorities. If the natural reservoir is in fact some other animal, positioning the first cases in each outbreak would still give a clue about what to look for."

Source: KTH The Royal Institute of Technology

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