Mutagenesis-Mediated Virus Extinction

One of the peculiarities of RNA viruses is their high mutation rate, which makes pathogens like HIV or Hepatitis C so elusive when it comes to vaccine design. A high mutation rate ensures that the virus can rapidly adapt to escape not only the host's immune response, but also antiretroviral treatments. Take HIV, for example: once inside the body, HIV evolves into numerous quasispecies -- new viral strains genetically distinct from the initial founder strain (the one that started the infection). That's why no single HIV strain can be used as a vaccine, as it wouldn't be protective against all possible strains. Furthermore, a cocktail of several drugs is needed in order to keep the viral load under control. When patients take one drug only the virus is able to rapidly find mutations that make it "immune" to the drug and hence make the treatment ineffective.

Last week I gave an introductory talk on both HIV and Hepatatis C and as I was describing the advantages of their high mutation rate, somebody in the audience asked, "Is there an upper limit on how high the mutation rate can be?"

The answer is: absolutely. You see, mutations happen at random. Some end up being advantageous, others will be deleterious. The advantageous one stay, the deleterious ones disappear because the viruses carrying them are non-viable. The population can tolerate a certain number of deleterious mutations, provided enough of advantageous ones appear at the same time in order to compensate for the loss. The effective mutation rate has to be high in order to ensure rapid adaptability, but if it ends up being too high deleterious mutations will prevail and the viral population will eventually go extinct.

So then the next natural question to ask is: can this be exploited as a new antiviral strategy?

This strategy exists and it's called "lethal mutagenesis" because its net effect is to decrease viral fitness by increasing the rate at which new mutations appear. By using mutagenic molecules, Moreno et al. [1] showed two possible outcomes in viral infections caused by the arenavirus lymphocytic choriomeningitis virus (LCMV): they either observed inhibition of progeny production and a decrease in viral infectivity, resulting in viral extinction, or a decrease in viral load. I found similar studies, spanning between 2001 and 2005, that used the same mutagen to attain extinction in the Foot-and-Mouth Disease Virus.

But how exactly do they increase the mutation rate? There are many kinds of mutagens. Ionizing radiations like X-rays, for example, are a familiar kind of mutagens: they cause mutations by damaging the DNA. However, here the task is subtler because we don't want to just damage the viral genome, we want to damage it in a way that it causes an increase in replication errors. The kind of mutagens used for this are called "base analogs", chemicals that can replace one of the usual nucleotides in the DNA, and when they do they cause copying errors to happen.

So, yes, a virus like HIV can use our own defenses to proliferate, since it attacks our immune system. But we can use its own defenses -- the high mutation rate -- to switch things around and try to defeat it.

[1] Moreno, H., Tejero, H., de la Torre, J., Domingo, E., & Martín, V. (2012). Mutagenesis-Mediated Virus Extinction: Virus-Dependent Effect of Viral Load on Sensitivity to Lethal Defection PLoS ONE, 7 (3) DOI: 10.1371/journal.pone.0032550

Is epigenetics new? Not to a "smart" influenza virus!

I was browsing the latest papers on Science when I read:

"By mimicking epigenetic regulation in human cells, one flu strain suppresses the expression of antiviral genes [1]."

Wow. Epigenetics and viruses? I had to read that paper!

I've discussed many times how gene expression in cells can be altered through epigenetic changes. The figure below, also taken from [1], shows one of the most common mechanisms by which cells alter gene expression: inside the nucleus, DNA is wound around proteins called histones. The addition of a methyl group (shown in blue in panel b), can alter the transcription of the gene.

In the figure, H3 represents the histone tail. This tail has two amino acids, lysine and arginine, which can be modified in a way that alters the interaction between DNA and the histones. These cause changes in the topology of the chromatin (the way the DNA is packaged inside the nucleus), allowing for certain regions rather than others to be accessed for transcription. If I just gave you a headache, think of chromatin as a tight yarn and you want to poke your finger inside to reach certain threads. The histone tail is like a "lever" that you can use to gain or lose access to the inner parts of the yarn. That's how the cell activates or deactivates genes.

"The ability of histone tails to guide gene function indicates the possibility of targeted control of gene expression by artificial or naturally occurring molecules that can structurally and/or functionally mimic the histone tail [2]."

The influenza A H3N2 subtype has a protein, NS1, that is not vital to viral reproduction but is known to suppress the host's response to the viral infection. In fact, without NS1, the viral infection is significantly mitigated. In a recent Nature paper, Marazzi et al. [2] found that NS1 carries a sequence that resembles the histone H3 tail. This mimicry supports viral infection by halting the transcription of genes essential to counteract the infection.

"We have shown that H3N2 influenza A virus interferes with host gene expression by exploiting the very basic principles of the epigenetic control of gene regulation. By mimicking the histone H3K4 sequence, which has a key role in positive regulation of gene transcription, the influenza virus gains access to histone-interacting transcriptional regulators that govern inducible antiviral gene expression."

Of course, these findings are very intriguing and they raise the question of whether this mechanism is novel to the H3N2 strain or not, and, also, what would happen if a particularly virulent strain like the avian flu would suddenly develop this mechanism as well. At the same time, this opens up new research on ways to attenuate viral infections by targeting the NS1 protein.

[1] Krasnoselsky, A., & Katze, M. (2012). Virology: Influenza's tale of tails Nature DOI: 10.1038/nature11034

[2] Marazzi, I., Ho, J., Kim, J., Manicassamy, B., Dewell, S., Albrecht, R., Seibert, C., Schaefer, U., Jeffrey, K., Prinjha, R., Lee, K., García-Sastre, A., Roeder, R., & Tarakhovsky, A. (2012). Suppression of the antiviral response by an influenza histone mimic Nature, 483 (7390), 428-433 DOI: 10.1038/nature10892

Genome, epigenome, mutations, epimutations... rethinking inheritance

I just learned a new word: epimutation. Genetic mutations occur in the DNA, while epimutations describe the transcriptional silencing of a gene that is normally active.

What's intriguing about epimutations is that even though they do not change the DNA, these changes can be transmitted from one cell to its daughter cells, a process called epigenetic somatic inheritance. There's another level of inheritance, which happens when such epigenetic changes are passed on from one generation of individuals to the next. This is a very intriguing concept because, since epigenetic changes don't affect the DNA, it is a non-Mendelian type of inheritance. Also, this type of inheritance is non-obvious because of a caveat called epigenetic reprogramming: all epigenetic marks are generally erased during gametogenesis and early embryogenesis so that the cells that will make a new individual can start afresh. If you think about it, it makes perfect sense: embryonic stem cells have the "potential" to become any kind of cell line and hence they have to start from an epigenetic "clean slate." So, in order for epigenetic inheritance to occur, an epimutation must escape epigenetic reprogramming.

"If the entire genome were reprogrammed in the germline it would be impossible for epigenetic modifications to be inherited. However there are epigenetic markers that can escape both incidences of reprogramming resulting in epigenetic modifications that persist in the somatic cells of the individual [1]."

In [1], Migicovsky and Kovalchuk review the different mechanisms by which epigenetic inheritance could arise: for example, you know how in all cells DNA is wound around proteins called histones? Well, it turns out that in sperm chromatin the majority of DNA is actually bound by "protamines," another kind of proteins that replace histones during spermatogenesis. However, a small percentage of histones are still retained in mature sperm and these histones could be responsible for epigenetic inheritance. In addition, there is methylation- and histone-mediated inheritance, which alter the gene expression patterns, and, finally, certain RNAs could be inherited through the germlines, again, making non-DNA changes inheritable.

Epigenetic inheritance has been documented in the case of MLH1, a gene located on chromosome 3. Individuals carrying a germline epimutation in this gene only have one functional copy of the gene and are at a higher risk of developing non-polyposis colorectal cancer:

"Studies have indicated that such inheritance is possible, with one family showing maternal transmission of the epimutation to the son, although the mutation was erased in his spermatozoa. In this case, the MLH1 epimutation that caused a predisposition to HNPCC in the mother was also present in the son, indicating he also had an increased risk of cancer. However, in her other children the epimutation was shown to revert to its normal state, indicating that the mutation was erased during reprogramming. These results indicated that germline transmission of an epigenetic state that confers disease susceptibility such as in the case of hypermethylation of MLH1 is possible. Overall, studies thus far have indicated that although epimutations are usually erased in the germline, they may be retained at a low frequency."

[1] Migicovsky, Z., & Kovalchuk, I. (2011). Epigenetic Memory in Mammals Frontiers in Genetics, 2 DOI: 10.3389/fgene.2011.00028

Different viruses, different replication mechanisms

I often talk about HIV because that's my research field. However, HIV is not the only virus for which we currently don't have a vaccine. A recent news post on Scientific American warned that while HIV-related deaths are going down, chronic hepatitis C deaths are on the rise. According to the World Health Organization:

"It is estimated that 3-4 million people are infected with HCV each year. Some 130-170 million people are chronically infected with HCV and at risk of developing liver cirrhosis and/or liver cancer. More than 350,000 people die from HCV-related liver diseases each year."

HCV has many similarities with HIV: they are both highly variable with comparable mutation rates, leading to multiple subtypes, and they are both RNA viruses with similarly sized genomes (~9,500 bases). They also have similar clinical patterns, as the acute phase (first few months) is either asymptomatic or very mild in both infections, and is characterized by a rapid ramp-up in viral load (levels of viral RNA per blood unit). However, while the HIV viral load, after reaching a peak, comes back down, the HCV viral load reaches a plateau and remains constant for many weeks. Eventually, only 20-30% of individuals infected with hepatitis C will spontaneously clear the virus and resolve the infection, whereas 70-80% will progress to persistent infection.

The biology of the two viruses is also very different, and if, like me, you thought RNA viruses are all alike, think again.

A virus needs to use the host cell machinery in order to reproduce. Different viruses have developed different mechanisms in order to do this. The key step is to use the genetic information they carry in order to make new viral proteins and hence new viral progeny.

Retroviruses are RNA viruses that, in order to produce new progeny, they need the DNA intermediate step. HIV is one of such viruses: once inside the cell, its RNA is transcribed into DNA by an enzyme called reverse transcriptase (also packaged inside the virion). The viral genome is then transported to the cell nucleus by another enzyme and is integrated into the host genome. This is a fundamental step for HIV, because it allows it to utilize the cell machinery in order to reproduce itself.

HCV also uses the cell machinery, but in a different way. Instead of using reverse transcriptase to turn the RNA into DNA, it uses a different enzyme, called RNA polymerase, which produces messenger RNA from which viral proteins are made. Through this step, HCV makes new negative RNA strands that serve as templates for the new progeny. The negative RNA templates stay inside the cell and continue to produce positive RNAs, while the positive strands may either be used to produce a new negative strand template, or they may be packaged into new virions, or they may be translated into proteins. All of this happens in the cytoplasm, and, contrary to HIV, HCV never enters the cell nucleus. HCV replication and post-translational processing happen in a "membranous web" called "replication complex," and then new virions are matured in the Golgi apparatus before being released outside the cell through exocytosis.

So, you see, though all retroviruses are RNA viruses, the opposite is not true. I learned something new today. Thank goodness I learned it in time for my talk on Thursday!

Ashfaq, U., Javed, T., Rehman, S., Nawaz, Z., & Riazuddin, S. (2011). An overview of HCV molecular biology, replication and immune responses Virology Journal, 8 (1) DOI: 10.1186/1743-422X-8-161

Young or old it doesn't matter: we need them both

To honor Brain Awareness Week I thought I'd try and discuss a neuroscience paper this week. It's not my field, so you'll have to be patient with me (and you experts out there are more than welcome to pitch in). I found a really fascinating story in the latest issue of Science [1] on the differences in information processing between "young" and "old" neurons. In order to understand the story, I had to take a couple of steps back and review a few things about the brain.

The hippocampus is the part of the brain that's responsible for learning, storing memories and associating them with feelings and emotions. Within the hippocampus lies the dentate gyrus, which is where adult neurogenesis takes place -- the formation of new neurons throughout adulthood. The middle layer of the dentate gyrus contains a type of neurons called granule cells. These are constantly generated and take a few weeks to develop and integrate in the dentate gyrus network. In [1], Marin-Burgin et al. asked the following question:

"Is it solely the continuous addition of new neurons to the network that is important, or are there specific functional properties only attributable to new granule cells (GCs) that are relevant to information processing?"

In order to answer the question, the researchers compared immature granule cells to mature ones in mouse hippocampus. The part that fascinates me the most about these experiments is that in order to "see" the different cells, these neurons are "retrovirally labeled to express red fluorescent protein." What this means is that a genetically engineered retrovirus that preferentially infects this type of cells is used to "infect" them and deliver the fluorescent proteins so that the neural activity can be visualized. Pretty cool, right?

Marin-Burgin et al. found that the dentate gyrus is made of a heterogeneous population of granule cells of different ages and that the different subpopulations have distinct activation thresholds. When given both excitatory and inhibitory input, the ratio of excitation to inhibition favors inhibition in mature granule cells, whereas immature cells have fewer inhibitory inputs (hehe, sounds familiar don't you think?). In other words, younger cells respond more easily and broadly, whereas older cells tend to be more specific. The fact that both are present at all times suggests that this range in different responses is needed for the correct functionality of the dentate gyrus, in particular for the correct storing and integration of novel information.

[1] Marin-Burgin, A., Mongiat, L., Pardi, M., & Schinder, A. (2012). Unique Processing During a Period of High Excitation/Inhibition Balance in Adult-Born Neurons Science, 335 (6073), 1238-1242 DOI: 10.1126/science.1214956

Human Immunodeficiency Virus model

Human Immunodeficiency Virus model

This is so darn cool! Well, okay, for an HIV scientist like me... But still, click on the link: it'll give you all the inside views of the virus, and then, if you click on "view labels" on the upper left corner, it tells you what you're looking at and the reference to the paper that describes it. So awesome to have it all conveniently in one picture!

How nucleosomes "protect" our DNA

Did you know that not all mutations happen at an equal rate? There are several kinds of mutations: substitutions, insertions, deletions, etc. Insertions and deletions happen when bits of DNA are either inserted or deleted, whereas substitutions happen when the overall length of the DNA locus doesn't change, but a base is substituted for another. As you all know, we have 4 nucleotides (A, C, G, and T), however, not all possible changes are equally likely. The most frequent substitutions are As with Gs and Cs with Ts.

Mutations happen because of errors in DNA replications or because of DNA lesions. These are chemical processes that are more or less likely depending on the circumstances. For example, DNA is "stronger" when it's a double helix, although occasionally the bonds between the two helices can locally denature, opening up a chance for a mutation to happen.

In all nucleated cells DNA is packaged inside the nucleus in units called nucleosomes: threads of DNA (~147 base pairs) wrap around "spools" formed by 8 protein units called histones. When the DNA is packed into nucleosomes it is more resistant and less prone to mutations. At the same time, chromatin, the assembly of all nucleosomes inside the nucleus, is hardly ever static. See this post where I discuss how nucleosomes are reassembled in order to promote the expression of certain genes versus others (a phenomenon called "chromatin remodeling"). A new study [1] published in the latest issue of Science investigates how the structure and assembly of DNA inside the cells affects the likelihood of certain mutations versus others. They found that nucleosomes act as regulators for substitution mutations, protecting DNA from damage. For example, compared to other DNA states, nucleosomal DNA undergoes 50% less C -> T mutations.

"Furthermore, the rates of G -> T and A -> T mutations were also about two-fold suppressed by nucleosomes. On the basis of these results, we conclude that nucleosome-dependent mutation spectra affect eukaryotic genome structure and evolution and may have implications for understanding the origin of mutations in cancers and in induced pluripotent stem cells."

Without getting into too many technical details, Chen et al. looked at the initial nucleosome profile from two replicates of the yeast Saccharomyces cerevisiae strain Y55, and then tracked subsequent mutations. They also looked at SNPs (single-nucleotide polymorphisms) in the germline of the Japanese killifish medaka. Germline cells are cells that give rise to oocytes and spermatocytes, hence mutations in this line are of evolutionary importance since they get carried on to subsequent generations.

We have revealed that nucleosomes, the most abundant eukaryotic protein-DNA complexes, likely function as a major regulator of substitution mutations in eukaryotes. Binding of proteins to DNA to suppress DNA breathing or to exclude endogenous mutagens may be how cells protect their DNA. However, DNA repair, which often works with varied efficiency between nucleosomal DNA and naked DNA, may also shape the base-specific mutation spectrum."

Chen, X., Chen, Z., Chen, H., Su, Z., Yang, J., Lin, F., Shi, S., & He, X. (2012). Nucleosomes Suppress Spontaneous Mutations Base-Specifically in Eukaryotes Science, 335 (6073), 1235-1238 DOI: 10.1126/science.1217580

Photo: light reflections (or is it refractions?) on a soap bubble. Shutter speed 1/125, focal length 100mm, F-stop f5, ISO speed 100.

GP 120!

I took the above photo yesterday. As I was processing it, I suddenly froze and thought, "GP 120!"

Check it out:

GP120 is the protein that sits on the outer shell (envelope) of HIV and binds to target cells. A trimer of three gp120 (together with three gp41, another protein) bound together forms the "spike" you see in the above picture.

Something tells me I've been working too hard if I suddenly see gp120 in tulips.
Fascinating, though, how these trimeric structures come up in nature, don't you think?

How are new viruses made?

I'm sure you are all familiar with H1N1, the influenza strain that emerged in 2009 and which contained genetic elements from four different strains: two swine flu strains, one avian flu strain, and one human flu strain.

How did this incredible mix-up happen?

One thing I've learned in the five years I've spent studying viruses is that these little things are genetic brewing machines (I just made that expression up, please don't quote me!). They can carry genetic material from different organisms, they can integrate in the host's genome, they can transport genetic material from one organism to another. The viral genome of a flu virus in particular is split in different portions called segments. Now suppose an avian flu virus and a swine flu virus infect the same hosts, and two viral particles coinfect the same cell inside the host. Yes, you've guessed it: the genetic segments from the two distinct viruses can indeed "reshuffle" and create a completely new virus. In the case of H1N1, this pattern of coinfection and "reshuffling" (called segment reassortment) happened more than once and across three different hosts: birds, pigs, and humans.

Reassortment of segmented viruses happens when two genetically distinct viral species coinfect the same cell and exchange genomic segments, a mechanism that ensures rapid novel virus creation. In the past, novel influenza strains have appeared when the virus's genomic segments reasserted with non-human flu genomic segments. The host's immune system may be prepared to recognize either strain but not a combination of both, hence the new virus can, potentially, evade adaptive immunity.

An interesting bit of the puzzle is that this reassortment does not appear to be random: there is a "reassortment bias", in other words, not all possible "reshufflings" of the genomic segments are equally likely to happen. There are constraints in terms of the genetic information that needs to be exchanged across the segments in order to make a new virus. The ability to predict which reassortments are most likely can help us be prepared for future outbreaks like H1N1.

In a recent PNAS paper [1], Greenbaum et al. use the mathematical framework of information theory to infer the viral populations produced by a coinfection out of the possible repertoire of progeny viruses. They look at quantities like entropy and mutual information to measure the genetic variation, predict which segments share relevant genetic information, and derive general segregation rules of how reassortment may happen.

"We study, for influenza and other segmented viruses, the extent to which a virus’s segments can communicate strain information across an infection and among one another. Our approach goes beyond previous association studies and quantifies how much the diversity of emerging strains is altered by patterns in reassortment, whether biases are consistent across multiple strains and cell types, and if significant information is shared among more than two segments. [1]"

Mutual information gives an upper bound on how much information strains can exchange. Pushing the rate of reassortment past this bound would disrupt viral segment communication and stop the creation of new virus. This is something I've heard about viral mutation rates, as well. Rapid turnover in genetic diversity is an advantage for tiny organisms like viruses and bacteria because it allows them to quickly develop escapes to the immune system: it's the Red Queen Effect I've talked about in the previous post. However, if this turnover it's too quick you get the opposite effect: when you go past the limit and start accumulating too much diversity, the population rapidly goes extinct because deleterious mutations happen more frequently than advantageous ones. This suggests that tweaking the diversity increase beyond this limit may be a novel defense strategy.

"Understanding how much these segments transfer information about their strain of origin, and to what extent this is possible, can ultimately lead to novel antiviral strategies."

Greenbaum, B., Li, O., Poon, L., Levine, A., & Rabadan, R. (2012). From the Cover: Viral reassortment as an information exchange between viral segments Proceedings of the National Academy of Sciences, 109 (9), 3341-3346 DOI: 10.1073/pnas.1113300109

It takes all the running you can do to keep in the same place

"Now, here, you see, it takes all the running you can do, to keep in the same place. If you want to get somewhere else, you must run at least twice as fast as that!"

~Lewis Carroll, Through the Looking Glass

The Red Queen Effect is a genetic effect named after Lewis Carroll's famous quote, "It takes all the running you can do to keep in the same place." As it turns out, Carroll's witty and paradoxical thinking fits viral host evolution: out of the whole viral population, only a few manage to infect new hosts -- these are the viruses that are fit enough to overcome the first hurdle (bottleneck) of "jumping" into a new host. Once there, though, these viral particles are not necessarily fit to survive the new host's environment because the defenses they have developed have been selected for in the previous host (this in genetics is called "fitness cost"). Therefore, they must mutate rapidly in order to acquire new defenses that will allow them to escape the new immune system.

Do you see why Carroll's Red Queen applies? A virus has to do all the running (mutating) it takes in order to keep (survive) in the same place (host).

Variety in hosts' immune responses is ensured by the MHC genes, the major histocompatibility complex genes in vertebrates. These genes, which are the most polymorphic among vertebrates, encode molecules found on all cell surfaces that mediate antigen presentation: when an antigen (any object, either a molecule or another organism, that is recognized as a "non-self" by the body) enters a cell, it is broken up and the bits of proteins are transported to the cell surface for "presentation" to the immune system. High variability in this class of molecules ensures that a wide range of antigens can be recognized and hence trigger the immune response. The high variability found in the MHC genes is the reason for the high variation in disease susceptibility in the population, for example, why a particular flu strain can keep one person in bed for a whole week, while another only gets a mild cold for a couple of days.

Just like the virus needs to do a lot of running in order to overcome the immune system, the immune system itself is at an advantage the more antigens it is able to recognize. So, you see, the Red Queen Effect, applies to both the host and the pathogen, leading to an antagonistic coevolution that ensures diversity in the MHC genes in the population.

A recent PNAS paper [1] investigates how this mechanism is maintained:

"One leading explanation, antagonistic coevolution (also known as the Red Queen), postulates a never-ending molecular arms race where pathogens evolve to evade immune recognition by common MHC alleles, which in turn provides a selective advantage to hosts carrying rare MHC alleles. This cyclical process leads to negative frequency-dependent selection and promotes MHC diversity if two conditions are met: (i) pathogen adaptation must produce trade-offs that result in pathogen fitness being higher in familiar (i.e., host MHC genotype adapted to) vs. unfamiliar host MHC genotypes; and (ii) this adaptation must produce correlated patterns of virulence (i.e., disease severity)."

In [1], Kubinak et al. describe how they repeatedly transmitted the same pathogen through different hosts (groups of genetically identical mice, each group carrying a different MHC family) and observed patterns of pathogen adaptation.

"Results from our experiments demonstrate that pathogen adaptation is host MHC genotype-specific. We conclude that pathogen adaptation to the familiar host MHC genotype produces trade-offs in pathogen fitness by reducing the reproductive output of adapted viruses when infecting hosts carrying unfamiliar MHC genotypes. Although previous work has shown that interactions between host and pathogen genotypes are important for determining patterns of pathogen fitness and virulence associated with infection, our dataset is unique in that it provides direct experimental support for fitness trade-offs associated with a pathogen’s adaptation to specific host MHC genotypes, thus confirming the first major assumption of the antagonistic coevolution model of MHC evolution."

With their experiment, Kubinak and colleagues proved that diversity in the MCH gene complex is maintained through the antagonistic coevolution between pathogen and host. This does not exclude other factors such as the heterozygote advantage and mating preferences, which have also been considered as likely explanations of the high variability in this gene family. As it often happens in genetics, the likely explanation is an interaction between all these phenomena and the hardest thing is to disentangle each contribution.

The authors conclude with one final thought, as their results suggest that populations with low MHC genetic diversity are likely to select for more virulent pathogens.

"If this suggestion is true, many livestock breeds and endangered species that exhibit reduced genetic diversity may be particularly sensitive to the consequences of rapid pathogen adaptation. Additionally, the prophylactic use of antibiotics on domesticated livestock places a selective pressure on pathogen populations to evolve antibiotic resistance, and as a consequence has been implicated in the emergence of antibiotic-resistant strains of human pathogens."

[1] Kubinak, J., Ruff, J., Hyzer, C., Slev, P., & Potts, W. (2012). From the Cover: Experimental viral evolution to specific host MHC genotypes reveals fitness and virulence trade-offs in alternative MHC types Proceedings of the National Academy of Sciences, 109 (9), 3422-3427 DOI: 10.1073/pnas.1112633109

MicroRNAs found for the first time in a retrovirus

MicroRNAs (miRNAs) are small non-coding RNAs that play a regulatory role in many cellular processes such as immune function, apoptosis and tumorigenesis. MicroRNAs are about 22 nucleotide long (on average) and they typically derive from primary transcripts "snipped" during a process called "endonucleolytic cleavage," which involves a protein that recognizes a double-helix RNA and cleaves the nucleotides in halves for degradation. MicroRNAs are post-transcriptional regulators, meaning they regulate what genes get transcripted by binding to their complementary RNA transcripts and thus preventing them to produce proteins.

Most eukaryotes, as well as many viruses, encode miRNAs. As you know, there are two kinds of viruses, depending on whether they carry DNA or RNA, and until now miRNAs had been found in DNA viruses only.

"Although limited studies exist, a preliminary model suggests that DNA viruses will use miRNAs for varied activities, including: regulation of latent/persistent infection, evasion of the innate and adaptive immune responses, and promotion of cell viability [1]."

A new study published in last week's issue of PNAS [1] reports the finding of miRNA in a retrovirus, namely the bovine leukemia virus (BLV), a virus that is associated with B-cell tumors both in cattle and sheep. How the virus initiates these tumors remains a mystery.

"Essentially all tumor cells are positive for the viral genome; however, very little, if any, viral mRNAs and proteins are detected in most cells [1]."

The finding that BLV encodes miRNAs is quite surprising because the general thought was that it would be deleterious for a retrovirus to encode miRNA, since it would have to come from the cleavage process I described above, and this could potentially affect the viral genome. In their study, Kincaid et al. identify a cluster of five miRNAs expressed from the BLV genome and also describe the mechanism by which these transcripts escape cleavage. Interestingly, one of the five miRNAs is functional and identical to the target portion in the host. The researchers demonstrate that the two miRNAs, the viral one and the host's, target transcripts that have been previously associated with B-cell cancerogenesis in mice, thus shedding new light on how the virus could initiate the cancer in the host.

"In summary, we demonstrate that an RNA virus expresses abundant, evolutionarily conserved miRNAs, including at least one that functions as an analog to a host oncogenic miRNA. These findings open up a role for noncoding RNAs in retroviral-associated tumorigenesis, and suggest the possibility that other retro- viruses exist that use noncoding RNAs in their infectious cycles."

Kincaid, R., Burke, J., & Sullivan, C. (2012). From the Cover: RNA virus microRNA that mimics a B-cell oncomiR Proceedings of the National Academy of Sciences, 109 (8), 3077-3082 DOI: 10.1073/pnas.1116107109