The Virus, the Koala and the Human Placenta
The country is a dwindling annexe to the factory,
Squalid as an after-birth.
Louis MacNeice, Autumn Journal (1938)
A poet chooses a metaphor or simile because it will be widely understood and easily related to the point he or she wishes to make. It is easy to see the afterbirth, the placenta, as squalid: the baby is passed around under adoring eyes while the placenta is disposed of. But the placenta is actually a biological marvel: the very organ that makes mammalian life possible.
The placenta’s job is to mediate between mother and baby. This is necessary because the baby incorporates the foreign genes of the father, and if it were to be in direct contact with the mother, it would be rejected as an alien graft.
But in a sense that Louis MacNeice could not have known, the placenta does have very murky roots which shed an entirely new light on the processes of life. It is now known that the mammalian placenta owes its existence to an ancient viral infection – somewhat like HIV – that left its DNA in the mammalian lineage and then mutated to a harmless form that found a function in the evolving placenta. About 8% of the human genome consists of viral remains like this; most have been complete disabled but a few have been co-opted to do a useful job for the host, the placental gene being the most notable so far.
Went down with a virus; going viral – everybody has some idea of what viruses are even though they were unknown 120 years ago and hardly anyone has ever seen one (they are too small to detect even with the most powerful light microscope – an electron microscope is needed). But, whether familiar like the cold bugs that come and go or life-threatening like HIV or Ebola, we see them as parasites that mean no good even when they are relatively harmless. The truth about viruses is much stranger than this.
Viruses are not alive: they are a kind of parody of life, stripped down to just a handful of genes and a protective protein coat, and missing all the cellular apparatus of life – they really are selfish genes. They are not viable on their own and to reproduce have to infiltrate their genes into another organism that does have the living machinery; they hi-jack it, and instruct it to produce more virus rather than the cell products it would normally make.
There are many kinds of virus but the ones with the most far-reaching consequences are the retroviruses. You’ve probably heard this term in the context of AIDS: the HIV virus is a retrovirus. What retrovirus means is that the virus inserts its genetic material into the host’s genes by a sneaky backdoor route: employing an enzyme called reverse transcriptase to write a copy of its own RNA genetic material into DNA. This Trojan Horse DNA then commandeers the host’s enzymes to make more viruses, which once again contain RNA as the genetic material and must find a new host to infect.
What is RNA? It is DNA that is synonymous with genes but in the 1950s it was realised that many viruses contain as the genetic material not DNA but its close but less stable cousin RNA.
In 1970 the discovery of this reverse transcription caused a sensation because it flouted what Francis Crick had called the “Central Dogma” of molecular biology. This asserted that the Genetic Code could only run in one direction: DNA → RNA → protein. Neither protein nor RNA could code for DNA. But reverse transcriptase creates a matching DNA from an RNA template, thus transgressing the Central Dogma. But it was the Dogma that had to give way: the process of reverse transcription has been a vital tool in genetic research for over 40 years..
As the 1970s went on and researchers were testing the implications of this process of reverse transcription, a new human plague was brewing. AIDS was first recognized in 1980-81 as a disease of homosexual men. In 1983 two separate research groups reported finding a retrovirus in AIDS patients. This was subsequently named HIV and since then a vast amount of research has resulted in detailed knowledge of the virus's structure and mode of action. HIV is a retrovirus that inserts its genes into human beings. The question arises: if it can do this could it also permanently enter the genome and become integrated? If so we would have a plague of even greater terror. HIV infects the body cells but it does not enter the germ cells: eggs and sperm. What about mothers passing AIDS to their babies? This is not genetic transmission – the baby is infected in the womb just as the mother had been infected sexually.
But here comes the startling bit: some retroviruses can enter the germ cells and thus be passed on to the next generation. In 1973 retroviral-like particles began to be found in the human placenta. Did this mean they were infected? Was this dangerous? Apparently not – the particle are found in normal placentas; they seem to belong there. The very next year tell-tale retroviral sequences were found in the human genome. How do we know this? Because retroviruses always contain a signature three genes: one to make the envelope protein, one to produce the reverse transcriptase enzyme, and one to form the retroviral core.
Retroviral sequences found in the genome today are no longer infectious, having been rendered innocuous by mutations. But could there have been a transitional period in which the virus was integrating itself but in some cases remained infectious? This seemed very likely. Was it also possible that in the case of the human placenta the retrovirus had integrated long ago but occasionally entire virus particle were produced like a ghostly afterbirth; the faint remains of the Big Bang of the original infection?
If a virus has succeeded in permanently infiltrating a host organism what next? Almost all such viral remnants in animal genomes are inactive. The host has succeeded in countering them and they have mutated and lost their infectivity.
Progress in biology can seem very slow when a single topic like this is followed. The mystery of the retroviruses found in the human placenta in 1973 has so far played out over more than four decades and is still ongoing. In the very first report the authors wrote: “A physiologic function for these particles is suggested”, meaning that what had once been an infective agent had perhaps been co-opted by the host – human beings – and put to some use. Verifying that hypothesis took a very long time.
In 1982 the presence of retroviral sequences in the human genome was confirmed. By 1987 that the gene was active in the placenta was established and a year later it became apparent that the gene was not active in choriocarcinoma, a cancerous disease of the placenta. By the early ’90s it was clear that a protein, produced by the viral gene fragment, played a key role in the healthy functioning of the placenta.
The placenta begins to form very early after gestation. The layer of foetal cells that implants into the womb has a strange property: all the cell walls dissolve and it in effect becomes one large cell with many nuclei.
The large fused-cell layer of the placenta is a kind of buffer zone between the immunologically different mother and foetus. There was an obvious potential role for the retroviral protein in this process. Retroviruses insert themselves into the host cells by fusing with the cell wall. They also suppress the immune reactions of the cell. So by 1995 it was thought that this retroviral fragment – which is shared with apes and monkey and seemed to extend back around 30 million years, before in fact the old and new world monkeys diverged – had a key role to play in mammalian birth.
According to Shakespeare it is the poet who “gives to airy nothing a local habitation and a name” but this is also how biologists operate. At first there is a strange finding, a mystery factor. Its nature is investigated and its composition and function becomes clearer. The mysterious factor in the placenta has been called many things over the years: type C particles, ERV3, HERV-W. But now that its contours are clear the protein produced by the relict retroviral gene has a stable name: syncytin, or rather syncytins 1 and 2, because there are two of them. In syncytins two of the three retroviral genes are still identifiable but they have been inactivated; only the gene that makes the envelope protein – the one that can dissolve cell walls to create the large multi-nucleate cell layer that forms the mediating layer between the foetus and the mother – is expressed.
In 2000, a paper in the journal Nature launched the syncytins onto the major stage of biomedical research. The next year it was found that syncytin 2 activity was reduced in the common disease of pregnancy: pre-eclampsia. In extreme cases the placenta detaches from the womb. The question was: just how important is this retroviral borrowing in human health: is it a matter of fine tuning or is it essential for normal birth?
Experiments showed that in the test-tube syncytin is capable of transforming other cell types into a large multi-nucleated cell, and fusion of human placental cells to form the large multi-nucleated cells was shown to be inhibited by an antiserum to syncytin.
The placenta is part of the definition of what it is to be a mammal: this co-opted viral gene thus seemed a clue to the evolutionary origin of mammals but, at the time of discovery, the researchers noted that the syncytin gene could not be found in other mammals. We now know that all mammals do have syncytins but they have evolved on more than one occasion. Human syncytins are known as syncytins 1 and 2; mouse syncytins as A and B.
In 2009, that syncytins are vital, at least in mice, was demonstrated by knocking out the syncytin genes. Knock-out mice are not especially charismatic animals but ones in which a gene under investigation has been disabled. The consequences of this are then monitored. When the syncytin gene is disabled, mice are stillborn because the cell fusion process in the placenta, facilitated by syncytins, does not take place. Although the mouse and human syncytin genes are different, researchers are confident that human syncytin in equally vital.
When the human genome was sequenced in 2001, the extent of viral infiltration was one of the first great revelations. In 1993, researchers had announced excitedly that as much as 0.1-0.6% of the human genome consisted of retroviral elements. With the full genome, that shot up to 8 %. Mostly, the viruses had been inactivated by mutations but their viral origins were indisputable, thanks to the presence of the three signature genes. To find all three genes in the human genome could not be a coincidence.
To put that 8% in perspective, the proportion of human DNA devoted to making proteins (thought for decades to be the sole purpose of DNA) is only about 1%. A massive 45% of the human genome consists of parasitic DNA of one kind or anther, including that 8% of retroviral elements.
Beyond the placental gene, were these other relict viruses in the human genome really dead or were they a potential source of disease – perhaps they were sleepers? In 2006 a dramatic piece of genetic detective work recreated an infective virus from a disabled human retrovirus. The virus in question HERV-K, active in some cancers, is less than 5 million years old. There had been 20 mutations since then and the most likely original virus was reconstructed by genetic engineering. And, yes, it was infective! With this demonstration it all became chillingly real. These really were the remains of viral infections, and they were a permanent part of being human. And, presumably, it wouldn’t necessarily take 20 mutations to reactivate one of them – plenty of evidence suggests that, in some cases, one might be enough.
Recent evidence suggests that two members of the retrovirus family HERV-K were still infective after the emergence of anatomically modern humans 200,000 years ago. So is retroviral insertion now over for good or could it happen again? Could it, in fact, happen with HIV and what would be the consequences? The HIV virus currently inserts itself into the adult human host genome but has not entered the germ line.
It could happen, because we can see genome insertion into the germ cells happening in a higher animal now: the koala. The koala has been called many things – cuddly, threatened, lazy, stupid, and bear (which is not) are high on the list – but that it should be at the cutting edge of biological research seems unlikely. But so it is.
The koala inspires affection because of its cute facial expression but it is, by all accounts, a rather sad creature. It is a marsupial, related to the wombat, and although its evolution is not well understood, its lifestyle, subsisting on eucalyptus, is thought to be a fairly recent specialisation resulting from climate change which led to Australian rain forest being replaced by eucalyptus forest. Eucalyptus is toxic to most predators but koalas have evolved the ability to digest the leaves. So they have the eucalyptus forest to themselves but there is a price. Eucalyptus is poor fare, low energy food, and the koala is thus a sluggish creature. It rests, motionless, mostly asleep for 16-18 hours a day. About 60% of its active waking time is spent feeding. Marsupial species often have an equivalent among mammals, and the closest mammal to the koala is the equally sluggish sloth.
It isn’t only the habits of the koala that reflect its poor nutrition. They are literally empty headed, 40% of the brain cavity being fluid and the brain itself a shrunken thing like a shrivelled walnut. This is not a very appealing picture but, superficially, koalas are charming. The young, called joeys, are only one quarter of an inch long at birth. They spend 6 months in the mother’s pouch, then 6 months riding her back, drinking milk, and eating eucalyptus. They take digested eucalyptus pap from their mother to acquire the enzymes they need to digest it.
The early years of colonisation were not kind to Australia’s native fauna and the koala was hunted almost to extinction for its fur in the early 20th century. With its meagre diet and small brain the koala was not best suited to the havoc that humans have wrought. But despite the poor hand nature has dealt it, when introduced to islands such as Kangaroo Island, off the coast of South Australia, the koala can ravage the eucalyptus forests because of lack of predation. The koala is now fiercely protected and even when it has become a plague, as it has on Kangaroo Island, culling is resisted by public opinion.
So far, this is just a normal tale of an endangered species in the 21st century but what is striking about the koala is the disease that is now cutting a swathe through its ranks. In 1961 two cases of leukaemia were reported in koalas. This was a first for koalas although not especially rare in animals, but there was more to come. By the 1980s it was apparent that 3-5 % of koala deaths in Queensland and NSW were caused by lymphomas and leukaemia. This incidence was high enough for researchers to suggest that a retrovirus might be responsible and this was confirmed in 1997.
Very soon, the koala retrovirus (KoRV) proved to have some unusual properties. Retroviruses are usually either in or out of the genome – an actively infective form or a disabled, integrated form. But some of the koalas had more varied numbers of the retroviral genes, some of which were whole and some of which were truncated. Stable it was not and this suggested that the virus might be in the process of integrating itself into the genome, crossing the line from external infection to internal genetic transmission. Here was a retrovirus entering a genome before our eyes, in real time.
By the mid noughties it was apparent that the virus was very recent and was sweeping through the population from the north downwards. The southernmost population, on Kangaroo Island, introduced in the 1920s, was free from the virus. In Queensland, to the north, the virus was deeply entrenched and was passed on in the genes; between the two extremes, the virus was part passed on as a normal infection, part incorporated in the genes.
The nature of the koala retrovirus, which causes immunodeficiency and vulnerability to infections and cancers in the animals, is curious. It is very closely related to the gibbon ape leukaemia virus (GALV) but there are no apes in Australia and no koalas in Africa or Asia. An intermediary is suspected, perhaps a bird.
What will be the koalas' fate? If this disease had taken hold before the era of conservation and molecular biology it would have taken a natural course. Perhaps koalas would have been wiped out but more likely the entire population would eventually have evolved to carry an inactivated form of the virus as junk DNA.
But for now, the disease cannot follow an entirely natural course. Attempts will be made to keep the Kangaroo Island population free from the virus. Whatever its future, the koala will always be famous for demonstrating a principle of evolution in action: the gradual incorporation of retroviral DNA into animal genomes.
The koala of course is not a mammal – it is a marsupial, in which the offspring is born as a hairless blind foetus. Marsupials do have a rudimentary placenta but it doesn’t fulfil the deeper nurturing role of the mammalian placenta. The full placental mechanism enables mammals to live for a long time in the womb and is obviously one of evolution’s crucial inventions. In many cases, marsupial and mammal species have converged independently on similar forms, through living in similar niches. But if placental mammals had not evolved it is unlikely that the marsupial line would ever have produced anything like a human being. The placental method was almost certainly vital to produce the large brain that is Homo sapiens' defining characteristic (remember the koala’s shrunken walnut of a brain).
But perhaps …just perhaps . . . In the same way that the mammals began to evolve and to colonize new niches after the extinction of the dinosaurs, perhaps a human extinction would find a rump population of koalas, having fought off and disabled KoRV, beginning to evolve through a novel use of the retrovirus? Its shrunken walnut brain would start to expand…You get the picture.
Why was there such potential in the small mammals that came to inherit the world after the dinosaurs? Other large life-forms such as reptiles were never likely to produce anything with the large brain of human beings. A reptilian egg has to contain all the nutrition to enable a viable young to be born. A developing brain of human size requires more nutrition than such a store can provide. To make a human being you first have to create a line of placental mammals.
A great deal of effort and money has been expended in an attempt to conserve the koala. This is because we have fellow feeling for furry animals. Marsupials such as the koala do not have all the attributes of mammals but they do give birth to live young, however small, and we find the way the baby crawls into its mother’s pouch for a period of suckling charming. Compared to the reproductive habits of other animals, the nurturing of live young in the womb, helplessness at birth and breast feeding are all warm, vibrant phenomena. An egg by comparison is just a hard mineral lump with edible contents.
But that warm, animal empathy is somewhat subverted if we consider that we and all the mammals owe our way of life to a chance infection more than 30 million years ago by a virus that merely wanted to propagate its alien genes. Some will find it distressing that the nurturing placenta, a vital part of the miracle of birth, comes from a hostile virus. It is a moment akin to the decentring people felt when we discovered that the cosmos did not revolve around the earth. No only are we very small and insignificant, we are not even ourselves: but part human, part virus. But we have been here before: we have known for decades that the embryo at between four and five weeks of age has tail vertebrae that normally are destroyed by programmed cell death but occasionally result in a tail at birth. Are we really rats? Of course not. Before that the embryo has gills, reminding us that we, like all land animals, had fishy ancestors. And beyond it all, our most distant ancestor that can be said to have been alive at all was a single-celled creature in the vast oceans: oceans which lapped on lifeless continents that bore no resemblance to the lands we live on now. It is an astonishing feat to have learnt so much about our origins. We should be proud of that and remember that the virtue lies in what emerged, not where it came from.
Various stark facts about the human genome such as this remind us of a profound error many people have made in the genomic era: the idea that we shall somehow “know who we are” at a deep level when we get to the bottom of the DNA. But the 98.4% genome similarity with chimpanzees, the 45% of the genome made up of parasitic transposable elements, the 8% composed of retroviral elements; the more than 200 house-keeping genes we share with all creation, including bacteria – these statistics argue against the primacy of DNA sequences. It is not a term I like, but the traits of higher animals are emergent properties that result from a particular form of organisation rather than a particular composition. A human being is a particular form of bipedal mammal just as a car is a rolling box on wheels that cannot be specified by the chemical composition of rubber, steel, petroleum, glass etc. Meaning resides in what the genes are able to create by subtle changes in timing rather than the small changes in the protein-producing genes themselves. The deep meaning of being human no more lies in the bases of DNA than the meaning of Shakespeare’s plays lies in the letters of the alphabet.
So to call the placental syncytin genes retroviral” or “viral” is in a sense misleading, although knowing where they came from is deeply fascinating. Once the retroviral genes had been co-opted for their placental role, their origin became irrelevant, just as the function rubber has in a rubber tree is irrelevant once the stuff is keeping your car on the road. It is almost certain that every one of our cells originates from the fusion of two kinds of primitive bacteria around 2.5 billion years ago. That does not make us bacteria. Primo Levi said:
The trade of chemist …teaches you to overcome, indeed to ignore, certain revulsions that are neither necessary nor congenital: matter is matter, neither noble nor vile, infinitely transformable, and its proximate origin is of no importance whatsoever.
He was writing of inert, mineral chemical matter, not life: although every atom has a history of passing through different minerals, from air to water, to land etc, its nature bears no trace of these transformations. Living tissue is different in that traces of the past, such as chunks of ancestral genetic code with its frozen accidents of mutations passed on, do remain but, unlike a chemical element, a gene has no essential nature – with a few base substitutions a gene can achieve a totally different function; as with the past history of chemical matter, the former context of DNA sequences is irrelevant. The regulatory genes that shape bodily organs are especially random in their mode of operation. They seem to work by chance proximity to a coding gene because of the complex way the genome is folded, with protein complexes shielding the core DNA. A region that happens to fold close to a protein coding sequence can exercise control over it often by means of a single mutation. By this means chemistry is mastered by geometry.
To return to the retroviral elements in the human genome, once the infective elements had been disabled they were no longer viruses but a useful tool lying around in the genome, waiting for a function. Evolution makes much use of ready-made bolt-on functions like this. Nature is largely modular, a kit of parts and one highly complex function can often be adapted to a new use. Nature, as François Jacob, the Nobel Prize winning molecular biologist famously said, is a tinkerer, a bricoleur.
Evolution is like the man who cannot throw anything away but leaves things lying around “because you never know when they might come in handy”. Jacob wrote:
In many instances, and without any well-defined long-term project, the tinkerer picks up an object which happens to be in his stock and gives it an unexpected function. Out of an old car wheel, he will make a fan; from a broken table, a parasol. This process is not very different from what evolution performs when it turns a leg into a wing, or a part of a jaw into pieces of ear.
In the tinkerer’s workshop there is an accumulation of junk, the large contingent of disabled viral genes, redundant genes from earlier phases of evolution, but there are also nuggets of gold: useful modules that often by the flip of a few base-change mutations in DNA can be put to some new use.
In the placenta, the infective elements of the virus were first disabled by mutations. Then the potential of the remaining envelope gene came into play. Every cell in our body contains retroviral DNA, but it has only been exploited, turned to a new use, where there was some gain. In the placenta, that cell-fusion property came into its own.
We are full of these genetic bolt-ons. Our energy comes from the ancient bolt-on of the mitochondrion, when one bacterial cell engulfed another and found it could be more useful intact than eaten. That was around 2.5 billion years ago. Bacteria and viruses are good loci for evolution to hone very precise functions, which then may find secondary uses. They can evolve very rapidly, as we know from antibiotic resistance and the annual evolution of new flu viruses. They are fast on their feet because they reproduce very quickly and can survive mass wipe-outs, which give mutations a better chance. Human beings have to wait 25 years for a new generation to try out a mutation, and despite the Four Horsemen, human populations have never been culled in anything like the way bacteria and viruses have. Many intricate cellular mechanisms must have evolved in this way. And once the mechanism is perfected it can often be used by a higher creature that lacks the bacterial/viral plasticity to evolve new functions from scratch.
There are countless other examples of the indirectness of nature’s means. There is no designer route to the creatures that appear to be so expertly designed. The ramshackle workshop of the genes is all there is.
In his poem ‘The Circus Animal’s Desertion’ Yeats wrote:
I must lie down where all the ladders start.
In the foul rag and bone shop of the heart.
It is not only the heart that is impure; all life is made from a tinker’s yard of scrap genes. They can become ennobled through incorporation into fine organisms but, as for the genes themselves, as Primo Levi said of all chemical molecules, their “ proximate origin is of no importance whatsoever”.
