The viruses inside us

Dendogram of endogenous retroviruses. Source: Wikipedia.

Last month I posted a discussion on a PNAS paper that reported the discovery of a new class of viruses, called pithoviruses, found in a layer of Siberian permafrost. In their paper [1], the researchers conclude:

"Our results further substantiate the possibility that infectious viral pathogens might be released from ancient permafrost layers exposed by thawing, mining, or drilling."

I found this possibility intriguing both from a scientific point of view as well as a sci-fi point of view: there are plenty of books out there on zombies and aliens, but what about ancient viruses that thawed from the ice thanks to global warming?

An attentive reader, though, didn't buy the sci-fi "threat" and asked in the comments whether viruses are necessarily bad. Normally we think of viruses as pesky little things. And while most will make us sick for a short time only, some can indeed be deadly, and others can inflict long-term complications.

The reader who asked that question, however, is absolutely right: over the course of evolution, viruses have been beneficial to us. Viruses have driven genetic diversity by transferring genes across species, and in fact, we still carry remnants of viral genes in our DNA, comprising roughly 8-10% of our genome. They are called "endogenous retroviruses", or ERV.

In the rest of this post I will address two questions:

• What are those viral genes doing in our genome?
• How did they get there?

What are viral genes doing in our genome?

Most of them are doing nothing. They are "deactivated", meaning they do not code for proteins. Our genome is made of many redundant elements that over the course of evolution were silenced because no longer useful, only to be turned on again later on when a new adaptation happened.

One such example is the placenta, where endogenous retroviruses have been found to be expressed [2-4] and play a role in the growth and implantation of the tissue. We can only speculate on why retroviral genes are expressed in the placenta, but the hypothesis is indeed quite interesting: in order to survive, retroviruses debilitate the immune system. In general, this is not a good thing for the body, except in one very special instance: an embryo is literally a parasite growing inside the mother's body. It carries extraneous DNA and, under normal circumstances, something carrying extraneous DNA would be considered an antigen and attacked by the immune system. Therefore, the expressed viral proteins found in the trophoblasts, the outer layer of the placenta, would have the role of suppressing a possible immune reaction against fetal blood.

Another property viruses have is that of cell fusion: they literally "merge" cells together into one membrane. A second hypothesis is that this property is used during the development of the placenta to build a barrier between the maternal circulation and the fetal circulation.

How did viral genes end up in our genome?

A virus enters the body of a host with the sole purpose of replicating. In order to do so, viruses hijack the cell's own replicating machinery. Retroviruses in particular carry strands of RNA which, once injected inside the cell, are turned into DNA that is then carried inside the cell nucleus and integrated into the cell's genome. This ensures that once the cell replicates, the bit of viral DNA is replicated too.

There is a special set of cells, however, such that when the virus infects them it literally gets stuck. These cells are the gametocytes, a.k.a. oocytes in women, and spermatocytes in men, which do not duplicate unless they get fertilized. But by then the virus is no longer active. It's literally stuck, in the sense that the integrated viral DNA now cannot replicate and cannot escape the host's DNA. It's just a bit of non-functional DNA that gets duplicated along as the embryo grows. The new individual now carries the viral genes in every cell of his/her body, even in the gametocytes, and hence the viral genes will be inherited by future generations as well.

And that's how viruses ended up in our genome a long, long time ago and have literally become "evolutionary fossils." In fact, by looking at these endogenous retroviral sequences, scientists are able to reconstruct the evolution of ancient viruses.

References

[1] Legendre, M., Bartoli, J., Shmakova, L., Jeudy, S., Labadie, K., Adrait, A., Lescot, M., Poirot, O., Bertaux, L., Bruley, C., Coute, Y., Rivkina, E., Abergel, C., & Claverie, J. (2014). Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology Proceedings of the National Academy of Sciences, 111 (11), 4274-4279 DOI: 10.1073/pnas.1320670111

[2] Emerman M, & Malik HS (2010). Paleovirology--modern consequences of ancient viruses. PLoS biology, 8 (2) PMID: 20161719

[3] Dunlap KA, Palmarini M, Varela M, Burghardt RC, Hayashi K, Farmer JL, & Spencer TE (2006). Endogenous retroviruses regulate periimplantation placental growth and differentiation. Proceedings of the National Academy of Sciences of the United States of America, 103 (39), 14390-5 PMID: 16980413

[4] Dupressoir A, & Heidmann T (2011). [Syncytins - retroviral envelope genes captured for the benefit of placental development]. Medecine sciences : M/S, 27 (2), 163-9 PMID: 21382324

The molecular evolution of the senses

Last week we learned that vertebrates react to smells and tastes using G-protein-coupled receptors (GPCRs), a family of proteins that "sense" molecules outside the cell surface and, depending on the molecule, activate a series of cascade events inside the cell which triggers the appropriate cellular response. This is how we distinguish good flavors from bad flavors and similarly with smells.

We also learned that tastes are not always shared across species. In fact, the genes that encode GPCRs have been turned on and off throughout evolution multiple times, allowing for example some species to be sensitive to certain tastes or smells or colors, while others aren't. How do we know?

The molecular evolution of sensory systems can be retraced by looking at two things in particular: (1) the multigene families that encode the smell, taste, and pheromone receptors; (2) pseudogenes, the remnants of once functional genes that have been silenced and/or replaced by new genes. I've talked about pseudogenes in older posts (look here and here). The DNA is often redundant and gene duplication events occur relatively frequently throughout evolution. Sometimes a copy carries a mutation that, if advantageous, may be picked up by a selective sweep. When that happens, the older, now redundant copy gets silenced and becomes a pseudogene -- a no longer coding portion of DNA. Through phylogenetic analyses, researchers can determine when these genes lost their functionality and understand how senses have evolved across species.

In [1] Emily Liman gives a beautiful example with vision: the photoreceptors in our eyes contain photopigments consisting of a GPC receptor called opsin. Humans, apes, and some primates have three distinct types of opsin, each able to maximally absorb either blue, red, or green light. This makes our vision trichromatic. Other animals like rodents, instead, are dichromatic: they only have two kinds of opsins, which maximally absorb either blue or red/green. Now, it turns out, the green opsin gene is nearly identical to the red opsin gene, making it likely that one derived from the other through a duplication event. On the other hand, humans have completely lost the capacity to detect pheromones, which is the function of the vomeronasal organ. The GPCRs in the vomeronasal organ are encoded by two gene families called V1R and V2R. Mice have 165 functional genes in the V1R family and 61 in the V24, whereas humans have 4 possibly functional genes in the former and none in the latter. However, we have roughly 200 pseudogenes in the V1R family, indicating that at some point in our evolutionary history these genes underwent a loss of function. Computational methods show that the loss of vomeronasal functionality in human evolution happened 25-40 million years ago, which happens to be the same timeline as to when trichromacy appeared.

"Interestingly, this is the same time when trichromacy appeared, suggesting that visual signaling may have replaced pheromone signaling. Indeed, catarrhine primates show prominent female sexual swelling and other sexual dimorphisms, which provide a visual signal of reproductive and social status. Thus, it is likely that as primates began to rely on these signals over chemical signals, the vomeronasal organ became redundant, and selective pressure was relaxed on molecules it uniquely expresses."

Similar observations can be made about the olfactory receptor genes: humans have 802 genes, of which ~50% are pseudogenes, versus the 25% of the 1,391 genes in the mouse, indicating that at some point in our evolutionary history selection on these genes was relaxed.

There have been evolutionary changes in taste sensation as well, and typically these changes reflect adaptive changes in diet.

"Taste allows animals to determine the nutritive content of food before ingestion: of the five identified taste modalities, three (sweet, umami, and salty) signal the presence of essential nutrients and lead to ingestive behavior. The other two modalities, bitter and sour, signal the presence of toxins or the spoilage of food, respectively, and, to most animals, are aversive."

Genes encoding the sweet receptors are well conserved across all land vertebrates with the exception of cats, whose sweet receptor T1R2 is a pseudogene (and therefore non-functional). three of the bitter receptors have become pseudogenes in humans and, furthermore, a polymorphism has been reported in the population which affects the way some of us perceive a molecule called phenythiocarbimide. This variation was also found in chimpanzee, which makes the polymorphism predate the divergence of the two species.

In conclusion,

"Expansion of the number of genes encoding sensory GPCRs has, in some cases, expanded the repertoire of signals that animals detect, allowing them to occupy new niches, while, in other cases, evolution has favored a reduction in the repertoire of receptors and their cognate signal transduction components when these signals no longer provide a selective advantage."

[1] Liman, Emily R (2006). Use it or lose it: molecular evolution of sensory signaling in primates Pflugers Arch. , 2 (453), 125-31 DOI: 10.1007/s00424-006-0120-3

Cats (and other carnivores) don't have a sweet tooth, they have a sweet pseudogene

Cats are insensitive to sweetness. Like all vertebrates, they react to smells and tastes using G-protein-coupled receptors (GPCRs), a family of proteins that "sense" molecules outside the cell surface. Depending on the molecule, GPCRs activate a series of cascade events inside the cell that triggers the appropriate cellular response.

There are five distinct flavors: sweet, salty, bitter, sour, and umami. We have different GPCRs for each different taste, and each group is encoded by a family of genes. Differences in taste perceptions reflect differences in these genes. For example, the genes encoding for the bitter taste receptors vary in sequence and number across species, most likely reflecting the ability of a certain species to detect foods that are toxic or harmful to them. Another family of genes, Tas1r, mediates the sweet taste, and one gene in particular, Tas1r2 is a psedugene in cats, which explains why they have lost the sweet taste receptor.

I've talked about pseudogenes in older posts (look here and here): the DNA is often redundant and gene duplication events occur relatively frequently throughout evolution. Sometimes a copy carries a mutation that, if advantageous, may be picked up by a selective sweep. When that happens, the older, now redundant gene copy gets silenced and becomes a pseudogene -- a no longer coding portion of DNA.

Back to cats: the fact that they possess Tas1r2, one of the genes encoding the sweet taste receptor, indicates that some "cat ancestor" had the fully functional gene and hence could detect sweet tastes. However, at some point down the line, the gene turned into a pseudogene and lost its functionality, making cats insensitive to sweet foods. Is this unique to cats? Many carnivores that have atrophied taste systems swallow their food whole and seem to be also likely to have pseudogenized taste GPCR genes (causing them to be insensitive to certain tastes). That's one of the hypothesis posed by Jiang and colleagues in a recent PNAS paper titled "Major loss in carnivorous mammals" [1].

"We found that seven of the 12 species examined from the order Carnivora -- only those that feed exclusively on meat -- had pseudogenized Tas1r2 genes as predicted. Furthermore, we confirmed our hypothesis that, in addition to the loss of Tas1r2, both the sea lion and bottlenose dolphin lack Tas1r1 and Tas1r3 receptor genes, suggesting an absence of both sweet and umami taste-quality perception. Additionally, we failed to detect intact bitter receptor genes Tas2rs from the dolphin genome, suggesting that this modality may be lost, or its function greatly reduced, in dolphins. Thus, taste loss is much more widespread than previously thought, and such losses are consistent with altered feeding strategies."

Jiang et al. sequenced Tas1r2 from 12 species within the Carnivora order and found that 5 had an intact gene, whereas 2 (the sea lion and the fur seal) had a mutation in the start codon (the first bit of the gene) that prevents it from being translated, making the gene no longer functional. Additional deletions in Tas1r2 lead into thinking that it has turned into a pseudogene in these two species. The Pacific harbor seal Tas1r2 revealed a frameshift mutation (a disruption in the "coding" into amino acids) and several early stop codons that would cause the relative mRNA to be incomplete and hence the gene defective. Similar off-reading-frame disruptive mutations were found in the remaining species (Asian small-clawed otter, spotted hyena, fossa, bottlenose dolphin, and banded linsang). With the exception of the sea lion and fur seal, none of the mutations disrupting the reading frame were shared between species. This is interesting, as it seems to indicate that the loss of functionality in Tas1r2 happened independently many times during the evolution of these Carnivora species.

They also did a phylogenetic analysis using Tas1r2 sequence data from 18 Carnivora species, of which 8 had a pseudogenized Tas1r2, and 10 had an intact one, and finally compared taste preferences between small-clawed otters (which have a defective Tas1r2) and spectacled bears (which, instead, have an intact Tas1r2). The statistician in me couldn't help but notice that they had only 2 otters and only 4 bears -- the small sample size red light went off in my head. That said, they saw that the otters saw no preference for sugar, whereas the bears showed a strong preference for both natural sugars and noncaloric sweeteners (hey, you never know, even bears may want to save a few calories here and there so they can indulge in others!). With the exception of cats, this was the first study to test taste preferences in animals with a defective Tas1r2.

Jiang, P., Josue, J., Li, X., Glaser, D., Li, W., Brand, J., Margolskee, R., Reed, D., & Beauchamp, G. (2012). From the Cover: Major taste loss in carnivorous mammals Proceedings of the National Academy of Sciences, 109 (13), 4956-4961 DOI: 10.1073/pnas.1118360109

Chimeras unveiled: genetics versus epigenetics

You think you know everything about chimeras? Well, think again: today I'm about to surprise you.

Let's start from the very beginning: in Greek mythology the Chimera was a monster, part goat, part snake and part lion.

Like with many other things, genetics borrowed the term to define organisms that are the result of genetically different tissues fused together. This happens at conception, when two fertilized eggs fuse together to form a single individual. Conceptually, it's the exact opposite of identical twins, where one fertilized egg splits into two identical individuals. Chimeric animals, for example, will present bits of fur of different colors. A chimeric person may show different pigmentation across his or her body. The individual will have two distinct DNAs in different tissues.

I'm sure so far I haven't told you anything new.

One day one of our experimentalist collaborators called to tell us they'd found a chimera. He was quite excited about the discovery. I scratched my head. Because you see, he was talking about HIV. And the thing with HIV is that it has one molecule of RNA. Just one, that's all there is. And so, how can a virus be the result of "tissues" coming from different genomes?

It turns out the definition is slightly different for viruses. A chimeric virus is a virus that has bits of extraneous DNA in its genome. Here I should be careful: HIV is a retrovirus, which means a free viral particle carries RNA, not DNA; however, once it enters the cell, an enzyme called reverse transcriptase turns it into DNA and, as DNA, it enters the host cell's nucleus and gets integrated into the host's DNA. This integration is what allows the virus to replicate. It's also what caused our chimeric virus to integrate in its own genome part of the host's genome.

The concept is used in gene therapy: a retrovirus is basically a shell (called envelope) with genetic material inside, and it's designed to inject the genetic material into the cell's nucleus. This is a fundamental step in the retrovirus's life because without it, it can't replicate. Many gene therapy clinical trials have exploited this mechanism by genetically engineering a chimeric retrovirus that carries human genes. Once the virus enters the nucleus, it delivers the new genes, thus "fixing" the problematic ones. I will talk more about gene therapy in a future post.

So now you've met a new type of chimera. Wait, it's not over yet.

Remember when I introduced the concept of epigenetics? Remember what pseudogenes are? They are ancestral or redundant parts of our DNA that are usually non-coding. We learned in those earlier posts that epigenetic processes do change during one's lifetime, and, as a result, pseudogenes can be activated and become coding genes. They are called chimeric genes.

An individual with chimeric genes is what I call an epigenetic chimera. The individual has the same DNA across all of his or her tissues, but some cells express genes that are otherwise non-expressed in the species.

In summary, we have three types of genetic chimeras: individuals with different DNAs; viral particles integrating different bits of extraneous DNA; and individuals expressing different chimeric genes.

Now that you know the different types of genetic chimeras, you are ready to learn why you and I are chimeras, too. 

Picture: Statue of Hutshepsut, Metropolitan Museum of Art, New York City. Canon 40D, focal length 85mm, shutter speed 1/10. Hutshepsut was a female pharaoh, often depicted in a masculine attire and with the typical pharaoh beard, symbol of pharaonic power.

The case of "junk DNA" and why it shouldn't be called junk: Epigenetics.

(This is part 3 of 4 in a series dedicated to "junk DNA". Links to the previous parts: Part 1, and Part 2.)

Last year I was diagnosed with thyroid disease. Despite feeling pretty crappy, I found the phenomenon extremely fascinating. Okay, I'll admit, I found it fascinating after my doc told me worst case scenario they'd remove the thyroid and I'd be as good as new (minus the thyroid, that is). Here's what happened: somehow, my immune system decided that my thyroid was some kind of foreign object that did not belong, and it started producing antibodies to destroy it. And I mean literally destroy it: left untreated, the antibodies will keep attacking the thyroid until it's gone.

How the immune systems knows "self" from "non-self" (and hence attacks foreign objects but, under normal conditions, not its own cells) is a fascinating topic and worth a post in itself (and I promise it'll come, just give me a few more weeks!).

For now, though, I want to focus on this: thyroid disease is a purely genetic disease. So, if it was encoded in my DNA, why did I end up getting it last year instead of having it since birth?

Epigenetics  holds the answer to my question (for the veterans in the field, please see my note below).

There was a nice article in the Time magazine a few months ago that described the concept really well: if you compare our body to a computer, genetics is the hardware and epigenetics is the software. Or, to use another analogy that my friend and fellow scientist/writer Ian Tregillis coined, if the genome is a four-note musical score, then the epigenome is the musician who interprets and executes the music.

"Epigenetics" is an umbrella term that encompasses all processes that regulate gene expression. In other words, what decides which genes are "turned on" and which are "turned off."

Think of en encrypted message. You don't know the meaning of the message until I give you the key. Depending on what key I give you, the message may change dramatically. DNA is the encrypted message. In order to "read" the message, i.e. the instructions on how to make proteins, we need a system capable of "translating" the message. It's a very delicate and complex system. And while our DNA is exactly the same in every cell of our body, the epigenetics is different.

Well, that's kind of obvious, isn't it? Think about it: how does a brain cell know to behave like a brain cell, and a skin cell to behave like a skin cell? After all, they have the same DNA. What differentiates them is the epigenetic processes that translate the DNA in each type of cell. The brain cell will have "brain genes" activated, and the skin cell will have the "skin genes" activated, while the others will be turned off.

So far so good. Still, how do you explain genetic diseases like diabetes showing up in adults rather than from birth? They are indeed encoded in the individual's DNA, but in a very subtle way. Mutations that sit there, waiting to go off. Waiting for the right change in the epigenetic process that will suddenly activate them.

Yes, that's exactly what happens: our DNA stays the same throughout our lifetime, but the way we express the genes can and does in fact change. Environmental stress is one of the major reasons affecting these changes [1]. Example: drought can cause certain plants to switch on pseudogenes regulating their capability of survival with less water [2]. The availability of food can induce analogous epigenetic changes in animals. Studies have shown that a pregnant woman's diet can activate pseudogenes not only on the baby, but the changes are actually inherited by the baby's babies as well [3]. Even though these are not genetic changes, hence they do not alter the DNA, still, they are in fact inheritable and it takes a few generations for the switches in gene expression to wear off [4].

So, think about it: (1) DNA doesn't quite dictate who or what we are. And (2) good ol' Lamarck was not so far from the truth after all, was he?

Back to my original question: thyroid disease was indeed "encoded" in my genome, but it was an epigenetic change in the way my genes were expressed that one day set my immune system off to an anti-thyroid mission.

What does this have to do with junk DNA?

Well, remember what junk DNA really is: it's non-coding DNA. Genes that are "turned off." But wait, we just learned that "turned off" or "turned off" is something that can change during one's lifespan. So, what we call "junk DNA" is something dynamical, something that when we look again tomorrow may have suddenly become functional because of the way DNA gets translated.

More and more studies are finding a link between cancer and mutations that sit in pseudogenes (non-functional genes that are part of the so-called junk DNA). At first this was quite surprising. If these genes aren't translated, how can they affect our body? Well, it turns out they are indeed expressed in cancer patients, giving origin to the term oncogene. In other words, the mutation is there, and it's not until an epigenetic change occurs and the pseudogene gets activated, that the disease takes off.

So, don't call non-coding DNA junk.

We need to study this part of our DNA, because it holds important information about our health. It also holds the key to our survival as a species by allowing us to adapt and change as the environment around us changes. And, finally, it holds our evolutionary history: we carry our ancestors, from viruses to bacteria to monkeys in our DNA.

Technical note: I am using the term "epigenetics" in a broad way, to include any of the following scenarios: post-replication DNA changes; post-transcription RNA changes; and, finally, changes in protein translation. The association between thyroid disease and epigenetics is purely my own, but an analogous conclusion has been reached for similar autoimmune disorders, where the immune systems fails to recognize self from non-self -- see this paper.   

REFERENCES:
[1] Inheritance of Stress-Induced, ATF-2-Dependent Epigenetic Change. Ki-Hyeon Seong, Dong Li, Hideyuki Shimizu, Ryoichi Nakamura, Shunsuke Ishii. Cell - 24 June 2011 (Vol. 145, Issue 7, pp. 1049-1061)

[2] Epigenetics in the extreme: prions and the inheritance of environmentally acquired traits. Halfmann R, and Lindquist S. Science. 2010 Oct 29;330(6004):629-32.

[3] Epigenomic disruption: the effects of early developmental exposures. Bernal AJ, Jirtle RL. Birth Defects Res A Clin Mol Teratol. 2010 Oct;88(10):938-44.

[4] Transgenerational Epigenetic Inheritance: Prevalence, Mechanisms, and Implications for the Study of Heredity and Evolution. Eva Jablonka and Gal Raz, The Quarterly Review of Biology. Vol. 84, No. 2 (June 2009), pp. 131-176

Picture: Rock. Canon 40D, focal length 85mm, exposure time 1/100.

The case of "junk DNA" and why it shouldn't be called junk: Redundancy.

(This is part 2 of 4 in a series dedicated to the concept of "junk DNA". Part 1 is here.)

Carl Sagan used this beautiful video to illustrate evolution:

(And Vangelis's soundtrack is the cherry on top!)

You might think that the same happens to DNA: one mutation after the other, DNA branches out just like the organisms in the video. That is not quite the case. Most of the information is saved, not erased. Why? Because that is the smart thing to do.

Mutations typically occur as random errors when cells duplicate. This often results in a new, non-functional gene. The old gene is still functioning, and the new one has a mutation that may or may not be deleterious. As mutations accumulate, things shift. The new gene may end up being functional, and, if the new mutation doesn't alter the information (what we would call a "silent" mutation), it will perform the exact same function as the old gene. That's what we call "redundancy," in other words, two or more genes sharing the same functionality. This is advantageous because if one suddenly loses its functionality, the system can revert to the old one to restore the information. It's the same mechanism used in CDs and DVDs, for example, so that you can hand them off to your kids and, unless they decide to use them as frisbees, a few scratches won't ruin your music or favorite movies.

What if the mutation was not silent and it did change the functionality of the gene?

First of all, it takes many mutations and many generations for this to happen. Sagan's video summarizes million of years in just a few minutes. But when it does happen, the new gene takes over and becomes functional. And the old gene? Still there, stored away. If you compare genes to switches, whenever a "new" gene arises, the old one is turned off and a new switch is made and turned on.

The result?

We all share most of our DNA with monkeys, giraffes, elephants, mice. What changes is which genes are "on" and which are "off." The non-functional genes that we share with other organisms are called "pseudogenes," and they are non-coding. What this means is that when DNA is unfolded and prepared for the retrieval of information to make the proteins that keep us alive, all those pseudogenes are tossed away. And that's what led to the term "junk DNA." But you see, pseudogenes have a very important role in evolution.

Imagine to toss a ball onto a rugged landscape. There are infinitely many paths the ball can take. Evolution is a rugged landscape and organisms are balls competing for the equilibrium niches. In an ever-changing landscape, saving the information can be vital. How did mammals end up back in the ocean? Because it had become advantageous and the information was already there. A few pseudogenes became functional again and the switch happened.

Again, these changes don't happen overnight. We are talking about hundreds of generations. And there is no intention behind the changes, only pure randomness driven by selection pressure from the environment. We are changing our planet a little too fast for evolution to save us. But if we had enough time, eventually our body would adapt to a CO2 laden atmosphere as the first micro-organisms that populated the Earth.

That's because Mother Nature took care of everything.

Picture: Mirror installation at the Metropolitan Museum of Art, New York. Canon 40D, focal length 66mm, exposure time 0.3 seconds.