Structure of an infectious prion

prion conversionPrions are not viruses – they are infectious proteins that lack nucleic acids. Nevertheless, virologists have always been fascinated by prions – they appear in virology textbooks (where else would you put them?) and are taught in virology classes. I’ve written about prions on this blog (five articles, to be exact – look under P in the Table of Contents) and I’m fascinated by their biology and transmission. That’s why the newly solved structure of an infectious prion protein is the topic of the sixth prion article at virology blog.

Spongiform encephalopathies are neurodegenerative diseases caused by misfolding of normal cellular prion proteins. Human spongiform encephalopathies are placed into three groups: infectious, familial or genetic, and sporadic, distinguished by how the disease is acquired initially. In all cases, the pathogenic protein is the host-encoded PrPC protein with an altered conformation, called PrPsc. In the simplest case, PrPSc converts normal PrPC protein into more copies of the pathogenic form (illustrated).

The structure of the normal PrPprotein, solved some time ago, revealed that it is largely alpha-helical with little beta-strand content. The structure of PrPSc protein has been elusive, because it forms aggregates and amyloid fibrils. It has been suggested that the PrPSc protein has more beta-strand content than the normal protein, but how this property would lead to prion replication was unknown. Clearly solving the structure of prion protein was needed to fully understand the biology of this unusual pathogen.

The structure of PrPSc protein has now been solved by cryo-electron microscopy and image reconstruction (link to paper). The protein was purified from transgenic mice programmed to produce a form of  PrPSc protein that is not anchored to the cell membrane, and which is also underglycosylated. The protein causes disease in mice but is more homogeneous and forms fibrillar plaques, allowing gentler purification methods.

prion structureThe structure of this form of the PrPSc protein reveals that it consists of two intertwined fibrils (red in the image) which most likely consist of a series of repeated beta-strands, or rungs, called a beta-solenoid. The structure provides clues about how a pathogenic prion protein converts a normal PrPC into PrPSc . The upper and lower rungs of beta-solenoids are likely the initiation points for hydrogen-bonding with new PrPC molecules – in many proteins with beta-solenoids, they are blocked to prevent propagation of beta-sheets. Once added to the fibrils, the ends would serve to recruit additional proteins, and the chain lengthens.

The authors note that the molecular interactions that control prion templating, including hydrogen-bonding, charge and hydrophobic interactions, aromatic stacking, and steric constraints, also play roles in DNA replication.

The structure of PrPSc protein provides a mechanism for prion replication by incorporation of additional molecules into a growing beta-solenoid. I wonder if incorporation into fibrils is the sole driving force for converting PrPCprotein into PrPSc, or if PrPC is conformationally altered before it ever encounters a growing fibril.


TWiV 406: Pow, right in the enteroids!

The TWiV team discusses eye infections caused by Zika virus, failure of Culex mosquitoes to transmit the virus, and replication of norovirus in stem cell derived enteroids.

You can find TWiV #406 at, or listen below.

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TWiV 405: All the world’s a phage

The TWiXers discuss a study on vertical transmission of Zika virus by Aedes mosquitoes, and uncovering Earth’s virome by mining existing metagenomic sequence data.

You can find TWiV #405 at, or listen below.

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Animal viruses with separately packaged RNA segments

dose-response-plaque-assayThere are many examples of viruses with segmented genomes – like influenza viruses – but these genomes segments are packaged in  one virus particle. Sometimes the genome segments are separately packaged in virus particles. Such multicomponent viruses are commonly found to infect plants and fungi, but only recently have examples of such viruses that infect animals been discovered (paper link).
Sequence analysis of viruses isolated from Culex mosquitoes in Central and South American Countries revealed six new viruses with segmented RNA genomes, which was confirmed by gel electrophoresis of RNA extracted from virus particles.
Some of the virus isolates appear to lack the fifth RNA segment, and the results of RNA transfection experiments indicated that this RNA is not needed for viral infectivity.
RNA viruses with segmented genomes are common, but in this case, the surprise came when it was found that the dose-response curve of infection for these viruses was not linear. In other words, one virus particle was not sufficient to infect a cell (illustrated). In this case, between 3 and 4 particles were needed to establish an infection. These findings indicate that the viral RNA segments are separately packaged, and must enter a cell together to initiation infection.
These novel viruses, called Guaico Culex virus (GCXV) are distantly related to flaviviruses, a family of non-segmented, + strand RNA viruses. They are part of a clade of RNA viruses with segmented genomes called the Jingmenvirus, which includes a novel tick-borne virus isolated in China (previously discussed on this blog), and a variant isolated from a red colobus monkey in Uganda. These viruses are also likely to have genomes that are separately packaged.
An interesting question is to identify the selection that lead to the emergence of  multicomponent viruses that require multiple particles to initiate an infection. Perhaps transmission of these types of viruses by insect vectors facilitates the introduction of multiple virus particles into a cell. How such viral genomes emerged and persisted remains a mystery that might be solved by the analysis of other viruses with similar genome architectures.

TWiV 403: It’s not easy being vaccine

The TWiV team takes on an experimental plant-based poliovirus vaccine, contradictory findings on the efficacy of Flumist, waning protection conferred by Zostavax, and a new adjuvanted subunit zoster vaccine.

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Whole plant cells producing viral capsid protein as a poliovirus vaccine candidate

poliovirusAlthough the use of the live, attenuated (Sabin) poliovirus vaccines has been instrumental in nearly eradicating the virus from the planet, the rare reversion to virulence of these strains has lead to the World Health Organization to recommend their replacement with inactivated poliovirus vaccine (IPV). Unfortunately IPV is also not without shortcomings, including high cost, failure to induce intestinal immunity, and the need to keep the vaccine at low temperatures. An experimental poliovirus vaccine produced in plants could overcome these problems.

A new vaccine candidate was made by producing the poliovirus capsid protein VP1 in the chloroplast of tobacco plants (nuclear-directed antigen synthesis is often inefficient). VP1 was fused to the cholera toxin B (CTB) subunit which allows good transmucosal delivery of the protein. Leaves were freeze dried, ground to a powder, mixed with saline and fed to mice after subcutaneous inoculation with IPV. The results show that boosting with the plant-derived VP1-CTB protein lead to higher antibody neutralizing titers (against all three poliovirus serotypes) both in the blood and in fecal extracts, compared with mice inoculated with IPV alone.

The VP1-CTP protein within lyophilized plant cells was stable for 8 months at ambient temperatures. If immunogenicity is maintained under these conditions, it would eliminate the need for a cold chain to maintain vaccine potency, an important achievement.

The authors propose that plant-produced VP1-CTP protein could substitute for IPV once the use of OPV is discontinued. Whether this suggestion is true depends on confirmation, by clinical trial, of these findings in humans. Furthermore, oral administration of VP1-CTP plant cells alone produces no serum neutralizing antibodies, and whether VP1-CTP boosts immunity in OPV recipients remains to be determined. Because VP1-CTP does not provide protection in children who have never received IPV or OPV, it cannot be used if poliovirus circulation continues indefinitely in the face of a growing cohort that has not been immunized with IPV or OPV. Nevertheless the technology has promise for the development of other vaccines that are inexpensive and do not need low temperature storage.

TWiV 402: The plight of the bumblebee

Polio returns to Nigeria, Zika virus spreads in Miami, and virus infection of plants attracts bumblebees for pollination, from the virus gentlepeople at TWiV.

You can find TWiV #400 at, or listen below.

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Non-fatal attraction

bee attractionVolatile organic compounds that are emitted by plants – which play important roles in attracting insects – can be altered by virus infection. Infection by cucumber mosaic virus (CMV) increases the emissions that attract aphids, but the virus-altered plant juices are not so tasty, so the insect quickly leaves to spread virus to other plants (listen to TWiV #70 for a full discussion of this finding). Plant pollinators can also respond to plant virus-induced volatile compounds (paper link)

Cucumber mosaic virus is a (+) strand RNA virus that is a pathogen of tomato plants. The virus is spread by aphids, and bumblebees increase fruit yield by buzz-pollination (tomato plants are self-pollinating but bumblebees cause increased seed production).

To study the attraction of bumblebees to tomato plants, the authors encased single tomato plants in a tower topped with a screen and a small cup of 30% sucrose (shown in photo: credit). This arrangement allowed volatile compounds to waft through the screen above the plant.

Bumblebees clearly preferred to visit the CMV-infected over the uninfected plants. They also shunned plants infected with a mutant of CMV that cannot antagonize the RNA interference system of the plant – a major defense against viruses. The results suggest that CMV somehow alters plant produced volatile compounds to attract bumblebee pollinators, and that production of these compounds is regulated by microRNAs.

These findings – that CMV infected plants attract bees via the production of volatiles under the control of microRNAs – were confirmed using Arabidopsis, a model plant which can be genetically manipulated.

Chemical analysis of the volatiles produced by infected and uninfected tomato plants revealed that virus infection reduced the levels of two terpenoids, 2-carene and beta-phellandrene. These compounds are known to repel bumblebees, leading to the suggestion that their reduction may explain why bees prefer infected plants.

Is attraction of bumblebees by viral infection random, or does it have a purpose? CMV infection of tomato plants decreases seed production, an effect that is reversed when bumblebees are attracted to the plants and pollinate them.

The results show that CMV infection of tomato plants causes the emission of volatile compounds that attract pollinating bumblebees, which negate the inhibition of seed production by infection.

Bumblebees do not transmit CMV, so how did this non-fatal attraction come about? One can imagine that at one time CMV infection of plants did not attract bumblebees, and that infection severely depressed plant production. Then a random viral mutant arose that could induce the proper volatiles to attract bumblebees. This change provided a selective advantage because plant seed production was restored by bumblebee pollination. This is called a ‘payback’ hypothesis: the virus has a place to replicate, and the plant lives on due to virus-induced volatile compounds.

I have a bit of trouble with this payback idea, because at the base of it are human-like intentions. Why do we assume that what drives evolution are forces that make sense to us? The plant-centric view is that it was not a CMV mutant, but a plant mutant that arose, which could make the proper bumblebee attractants upon CMV infection. The selective force to maintain such a plant is very clear and involves no anthropocentric ‘payback’.

Whatever the origin of this non-fatal attraction, it merits further study, not only for developing better pollination methods, but for understanding the viral-host symbiosis.

Zika Virus in the USA

On this episode of Virus Watch we cover three Zika virus stories: the first human trial of a Zika virus vaccine, the first local transmission of infection in the United States, and whether the virus is a threat to participants in the 2016 Summer Olympic and Paralympic Games.

TWiV 401: Vector victorious

Zika virus spreads in the USA, a Zika virus DNA vaccine goes into phase I trials, and how mosquito bites enhance virus replication and disease, from the friendly TWiFolk Vincent, Dickson, Alan, and Kathy.

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