TWiV 452: Kiss that frog

Lynda Coughlan joins the weekly virtual bus companions for a discussion of a host defense peptide from frogs that destroys influenza virus, and mouse models for acute and chronic hepacivirus infection.

Click arrow to play
Download TWiV 452 (68 MB .mp3, 113 min)
Subscribe (free): iTunesRSSemail

Become a patron of TWiV!

Show notes at microbe.tv/twiv

Kermit’s urumi

Hydrophylax bahuvistaraFrogs don’t get flu (as far as I know) but their skin contains a peptide that inhibits the replication of influenza virus (link to paper).

Frog skin contains host defense peptides (HDPs), part of the innate immune defenses of many species. They were first found in amphibians by Michael Zasloff, who, as part of his research, performed surgery on frogs and then returned them to an aquarium – which was not sterile. He wondered why the frogs always healed without signs of infection, which lead him to discover the antimicrobial peptides, called magainins, in frog skin. HDPs had been first discovered years earlier in the silk moth.

Amphibian HDPs are active against bacteria, fungi, viruses, and protozoa. To discover HDPs that inhibit influenza virus, 32 HDPs from skin secretions of the Indian frog Hydrophylax bahuvistara were screened by mixing them with virus followed by a plaque assay. One peptide was found to potently inhibit influenza virus replication without cell toxicity. It was called urumin, after the whip sword known as urumi.

Urumin inhibits infectivity of influenza H1N1 viruses far better than H3N2 viruses. The reason is that the peptide targets the viral H1 hemagglutinin, one of two glycoproteins in the viral envelope. Furthermore, the peptide appears to interact with the conserved stalk region of the HA glycoprotein, and not with the globular head.

Currently two different antiviral drugs, oseltamivir and relenza, are used to control influenza virus infection. Viruses resistant to these drugs were still inhibited by urumin, indicating that should urumin ever be licensed, it would be useful in the event that oseltamivir and relenza resistant viruses became more common.

Examination of urumin treated virus particles by electron microscopy revealed that they are disrupted by the peptide. How urumin breaks influenza virus particles is not known. However, the HDP nisin destroys bacteria by first binding to a bacterial membrane component, then moving into the membrane. After binding to HA, urumin might in a simlar way disrupt the membrane of influenza virus particles.

Urumin also reduced disease, death, and the amount of virus in the lung in mice intranasally infected with influenza virus.

These observations suggest that urumin is worthy of additional study as an influenza virus inhibitor. HDPs are attractive antimicrobial compounds because resistance to their mechanisms of action is lower than for other types of inhibitors. However, enthusiasm for urumin is dampened because, despite extensive study, no HDP has yet been approved by the US Food and Drug Administration for use in humans. The obstacles to therapeutic success of HDPs have not been identified.

Ancient proteins block modern viruses

T7-like virusCould ancient host proteins contribute to the replication of a modern virus? The answer is, not very well (link to paper).

Viruses are obligate intracellular parasites, which means that they have to get inside of a host cell to produce more viruses. The genomes of all viruses, even the biggest ones, do not encode anywhere near the number of proteins that are needed to replicate. The cell provides thousands of proteins that are involved in energy production, membrane synthesis, protein synthesis, transport, and so much more.

The difficulty in studying ancient proteins is that none of them exist. But we can make good guesses about what very old proteins might look like, by examining modern proteins, seeing how they vary among organisms, and calculating how they might look like billions of years ago. The field of predicting what ancient proteins might look like is quite active.

Investigators have predicted what ancient versions of a cell protein called thioredoxin might have looked like. They have synthesized such ‘ancient’ thioredoxins and shown that they are stable and active. Thioredoxins are found in nearly all organisms, where they act as antioxidants.

Ancient thioredoxins that have been synthesized include those from the last common ancestors of bacteria; of archaea; and of archaea and eukaryotes (all around 4 billion years old); the last common anestor of cyanobacterial, deinococcus, and thermus groups (about 2.5 billion years old);  the last common ancestor of gamma-proteobacteria; of eukaryotes; and of fungi and animals (around 1.5 billion years old).

These ancient thioredoxins work in a modern E. coli. This bacterium has two thioredoxin genes, and if they are both deleted, growth occurs, but very slowly. If genes encoding ancient thioredoxins are introduced into these mutated bacteria, they can compensate for the growth deficiency. The older thioredoxins (4 billion years) compensate less well than ones that are closer in time (1.5 billion years).

It’s amazing that an ancient protein can work in a modern E. coli. But could ancient thioredoxins support viral growth?

Thioredoxin from E. coli is an essential part of the DNA polymerase complex of the bacteriophage T7 (pictured – image credit). This virus does not form plaques on E. coli lacking the two thioredoxin genes. The only ancient thioredoxin gene that allows phage T7 plaque formation is from the last common ancestor of cyanobacterial, deinococcus, and thermus groups, which is about 2.5 billion years old and has 57% amino acid identity with the E. coli enzyme. But the effienciency of plaque formation was very poor – about 100 million times worse than on regular  E. coli. None of the older thioredoxins worked.

Why would an ancient thioredoxin work for E. coli but not for bacteriophage T7? Over billions of years, thioredoxin evolves but it must still be able to carry out its function for E. coli. The viruses that infected bacteria 4 billion years ago were very different from contemporary viruses, and so the ancient thioredoxin does not work for modern viruses. Today’s thioredoxin could change so that it would not support T7 replication – as long as the enzyme still works for E. coli.

The authors of this work view it as a proof of principle: that virus growth is not supported by an ancient version of a modern protein required for virus replication. They would like to apply this approach to produce plants that are resistant to viruses, which have serious effects on global agricultural productivity.

I think the work is amazing not only because an ancient protein can be made, but it supports growth of the host and not that of a virus. It might therefore be possible to reconstruct the host-virus arms race, starting from ancient proteins. In this race, the gene encoding an essential cell protein can evolve so that it no longer supports virus replication. Next, the viral genome changes to adapt to the altered cell protein. And so the game goes back and forth.

The authors have shown that they can select mutant bacteriophage T7 isolates that replicate in the present of an ancient thioredoxin. This result suggests that it might be possible to reconstruct host-virus arms races beginning with an ancestral host protein. If we can make an ancient protein, could we also make an ancient virus? Why not?

TWiV 450: Ben tenOever and RNA out

Ben tenOever joins the TWiVoli to discuss the evolution of RNA interference and his lab’s finding that RNAse III nucleases, needed for the maturation of cellular RNAs, are an ancient antiviral RNA recognition platform in all domains of life.

 

Click arrow to play
Download TWiV 450 (58 MB .mp3, 96 min)
Subscribe (free): iTunesRSSemail

Become a patron of TWiV!

Show notes at microbe.tv/twiv

A virus with a green thumb

PoxvirusI just love it when long standing mysteries in virology are suddenly solved, typically by the use of new technologies. In this story, the long standing mystery was why poxvirus mRNAs have a stretch of poly(A) in their 5′-noncoding regions. The answer is that it allows the ribosome to preferentially translate these viral mRNAs over those of the host (link to paper).

Ribosomes, the sites of protein synthesis, are very large assemblies of RNAs and proteins. A ribosome-associated protein called RACK1 is the major player in this story. This protein was previously found to be important for translation of viral RNAs by internal ribosome entry, a process in which ribosomes bypass the 5′-cap structure on mRNAs.

Cells lacking the gene encoding RACK1 seem to be just fine – they grow normally. This result would suggest that RACK1 is not needed for translation of mRNAs via the 5′-cap structure. But the translation of mRNAs of vaccinia virus, a poxvirus, is blocked in cells lacking RACK1. More specifically, the viral mRNAs produced later in infection cannot be translated.

This effect of RACK1 on vaccinia virus mRNA translation prompted a closer look at the protein in virus infected cells – which revealed that it is phosphorylated by a viral protein kinase. Phosphorylation of RACK1 makes the ribosomes preferentially translate vaccina virus mRNAs – an effect that is completely dependent upon the poly(A) in the 5′-untranslated region! Transfer of this poly(A) sequence to a non-viral mRNA enhanced its translation in cells in which RACK1 is phosphorylated.

The amino acid sequence of RACK1 that is phosphorylated is within a loop that contacts the 18S ribosomal RNA subunit. An examination of RACK1 proteins from different species reveals that in plants, unlike in mammals, this loop contains a stretch of negatively charged amino acids. Because a phosphate is negatively charged, it made perfect sense to see if the plant loop sequence, when transferred to mammalian RACK1, could stimulate translation of poly(A) containing mRNAs. It did!

In other words, phosphorylation by a vaccinia virus protein kinase makes RACK1 plant-like! Which is why the authors called their paper ‘Trans-kingdom mimicry underlies ribosome customization by a poxvirus kinase”. Exactly what RACK1 protein is doing in plants is a burning question, as is how RACK1 recognizes mRNAs containing a poly(A) leader.

Phosphorylation of RACK1 by the vaccinia virus kinase explains why viral mRNAs with poly(A) leader sequences are preferentially translated in infected cells (late viral mRNAs have this unusual leader). The presence of poly(A) in the 5′-ends of late vaccinia virus mRNAs is considered to be a consequence of polymerase slippage – but it is clearly not a mistake. At one time, long ago, a polymerase might have slipped for the first time, but the resulting poly(A) in the mRNA conveyed a selective advantage that remained. Today I would no longer call the addition of poly(A) to vaccinia virus mRNAs an error!

Why did it take so long to figure out the role of poly(A) at the 5’-end of vaccinia virus mRNAs? The right technology was not available – the key ones were the ability to knock out specific genes in cells, to knock down mRNA levels with RNA interference, and to identify the sites of RACK1 phosphorylation by mass spectrometry. These are not only recently developed techniques, but they have become widely accessible. But don’t forget the use of long-ago isolated vaccinia virus mutants of the protein kinase that were an essential part of this story.

Rich Condit, a poxvirologist, joined Nels Elde (also a poxvirologist, though he dabbles in other systems) and me to discuss this very cool paper on episode #21 of TWiEVO, This Week in Evolution. Rich had some very good insight on this paper; plus he bristled twice during the episode. You’ll have to listen to find out why.

Image credit.

 

TWiV 449: The sound of non-silencing

The TWiV Council explores the finding that facial appearance affects science communication, and evidence that RNA interference confers antiviral immunity in mammalian cells.

Click arrow to play
Download TWiV 449 (62 MB .mp3, 102 min)
Subscribe (free): iTunesRSSemail

Become a patron of TWiV!

Full show notes at microbe.tv/twiv

The Traditional Lecture is Not Dead. I Would Know – I’m A Professor

Virology 2017Wired Magazine recently published an article with a headline distinctly opposite of mine, which claims that the traditional lecture is dead. I disagree, and here is why.

The thesis of the article, by Rhett Allain, is that modern technologies have made the traditional lecture obsolete. The traditional lecture is one during which a teacher stands at the front of the room and ‘disseminates knowledge to students’. Allain claims – rightly so – that animated videos like The Mechanical Universe are far more engaging. He suggests that, to teach physics, just show the students episodes from this show. If they have questions, just pause the show.

He claims that showing these videos – or equivalents for other subjects – beats most lectures. Lectures in which teachers drone on and on.

Well guess what – I teach a virology course at Columbia University, and at the end of the year, most of the students say its one of the best, or the best class they have taken in their college years. I don’t show The Viral Universe or any other videos during my class. I talk to the students about my knowledge of viruses, gained from researching them for over 30 years.

Not every virology lecturer has my experience in the field. Many of them learn virology from a book. I agree that lectures given by those individuals are dead.

I do record each lecture and post them at YouTube, so that the students in the class, or anyone in the world for that matter, can watch them. It’s a new technology that Allain likes. I like allowing the students to time-shift their learning: some never come to class. But it’s still me making the videos and sharing my knowledge via a traditional lecture format.

Allain is also fond of the flipped classroom – assign a video for students to watch before class, and then use class time to discuss it. I love this idea. But I still think that for my introductory virology class, it’s better for me to talk to them. To walk around the room, without notes, look them in the eye, and muster all my passion and love for the field and send it their way. And don’t think that doesn’t matter – many of my students tell me that my passion for the subject is what makes them interested in viruses.

Research says that most students learn better by doing. I do pause a few times during each lecture to have students complete an online quiz – something Allain also likes. It gives me time to see if what I’m saying is sinking in, and to clarify complex material.

When I lecture, students come to me afterwards with questions, and some even walk with me to the subway, to talk about viruses. How can a video provide that experience?

Allain’s response might be that if anyone wants to teach a virology course, just play my lectures and discuss them in class. I’m all for that. But every spring semester, I’ll be in front of the class, talking about viruses, and making new videos. There is no substitute for a expert who is passionate about their subject. I realize that every physics course can’t be taught by Einstein, but he can teach at least one, and the students at his university will love it.

Not every passionate researcher will make a great lecturer, and for them,  videos and flipped classrooms are a great way to teach. But for those passionate researchers who can teach – why not put them in front of a class and inspire the next generation? I do it every year.

TWiV 448: Mavis the Structure Maven

From ASV 2017 in Madison, Wisconsin, the complete TWiV team speaks with Mavis Agbandje-McKenna about her career and her work solving virus structures by x-ray crystallography and cryo-electron microscopy.

Click arrow to play
Download TWiV 448 (40 MB .mp3, 67 min)
Subscribe (free): iTunesRSSemail

Show notes at microbe.tv/twiv

Become a patron of TWiV!

TWiV 447: Un-impacting an elephant

The glorious TWiVerati un-impact their email backlog, anwering questions about viruses, viruses, viruses, viruses, viruses, and more. You should listen – our fans ask great questions!

Click arrow to play
Download TWiV 447 (67 MB .mp3, 110 min)
Subscribe (free): iTunesRSSemail

Show notes at microbe.tv/twiv

Become a patron of TWiV!

TWiV 446: Old sins die hard

The TWiV hosts review an analysis of gender parity trends at virology conferences, and the origin and unusual pathogenesis of the 1918 pandemic H1N1 influenza virus.

Click arrow to play
Download TWiV 446 (68 MB .mp3, 112 min)
Subscribe (free): iTunesRSSemail

Become a patron of TWiV!

Show notes at microbe.tv/twiv