Viruses that do everything the other way around
Retroviruses
A lecture by Greg Towers, Professor of Molecular Virology at University College London, has been published on the PostNauka website.
A class of viruses is called retroviruses because they do everything the other way around. The concept of "retro" is due to the fact that retroviruses have RNA in their genome, which they turn into DNA. Ordinary cells turn DNA into RNA, but never the other way around. Retroviruses do the opposite, and are therefore called retroviruses. All retroviruses perform this practice, which is called reverse transcriptase. They have two strands of RNA, which they convert into double-stranded DNA. Then they transfer this double-stranded DNA into the cell nucleus and embed it into the host genome. Thus, the retrovirus genome becomes part of the host genome, and the cell will never be able to get rid of it. The only way to get rid of the retrovirus is to kill the cell. That's exactly what the immune system does.
There are many different retroviruses. Many animal species have retroviruses. They are very zoonotic. Retroviruses are able to jump from view to view. This is their distinguishing feature. We assume that over millions of years of evolution, they jumped from one species to another, which led to the "Black Queen effect". If the virus is pathogenic, it infects the species and puts selection pressure on it. Many members of this species will be killed by the virus. This will lead to selection pressure, the purpose of which is to become insensitive to this infection or virus.
Since retroviruses are pathogenic, they lead to an evolutionary effect, or the "Black Queen Effect". A retrovirus infecting a species can have a pathogenic effect on that species in such a way that many people and many members of a particular species will be infected and subject to selection pressure. The most susceptible to this virus will die, and the most resistant will survive. Eventually, the entire species will become immune to the virus. Then the virus will undergo evolutionary selection pressure, change and re-infect the species or switch to another one. For a long time, the retrovirus can jump between different species, or it can touch some species and leave again, which will lead to an alternative evolution, which was called the "Black Queen Effect" by Lee van Valen.
One interesting feature of retroviruses is that we can understand their evolution and the evolution of our cellular defenses. The human immunodeficiency virus came to us from primates. The most common type of HIV is called HIV-1. It accounts for approximately 60 million human HIV infections. This is almost an isolated case when the chimpanzee virus struck a human and began to spread among the human population. We know that the direction of infection is exactly this – from chimpanzees to humans – because there are more types of this virus in chimpanzees than in humans.
There is another type of HIV, called HIV-2, which came to us from African monkeys, namely the smoky mangobey. And again, there are many more varieties of this virus in mangobeys than in humans. This tells us that the transfer of the virus occurs from monkeys to humans. HIV-2 causes a similar disease as HIV-1 in about 20-30% of people. However, most people do not experience any significant symptoms after contracting HIV-2. Therefore, one of the important issues of HIV biology is to find differences between the virus that infected 60 million people and the fact that it did not infect even about that number.
Primates have similar viruses. Moreover, most African primates have a virus that is related to our HIV-1. We usually name these viruses according to the species in which we found them. The chimpanzee virus is called VIO (SIV) – monkey immunodeficiency virus (simian immunodeficiency virus). In that case, do chimpanzees have AIDS? This is not completely clear. Not all chimpanzees are infected. There are certain territories where infected chimpanzees live. But since they do not live the lives of people, do not lead a refined lifestyle, but, on the contrary, live a more difficult life, they die much earlier, it becomes very difficult to follow them and find out if they have this disease.
Because of this, for a long time we thought that they did not suffer from any diseases, because they do not have such a strong immunodeficiency as humans. But recently we have begun to think that they also have this disease, perhaps in a less severe form. Since they do not live long, they do not have to suffer from the symptoms that a person experiences.
Thus, it is not fully known what happens to retroviral infection in the body of monkeys. In African monkeys, the virus practically does not cause any diseases, so it seems that there is an adaptation of both the carrier and the virus itself on the principle that a monkey can be infected, but not suffer from diseases. They can get infected at a fairly early age, so they may have a virus in their body, but at the same time they do not feel significant consequences for their lives.
Among other species, retroviruses have been carefully studied in mice. This was done mainly because retroviral infection in mice can cause cancer. The mouse is infected with a retrovirus, which is usually called a gamma retrovirus. It turns out that this retroviral infection causes cancer in mice. People who studied cancer in the 1950s and 1960s, that is, at the very beginning of such studies, raised a mouse until it became very vulnerable to this disease, and then tried to find out why these mice develop cancer. It turned out that they were getting cancer because they were infected with a retrovirus. These retroviruses carried genes (oncogenes) that caused cancer. Thus, all the primary studies of retroviruses were aimed at understanding how cancer works and what causes it.
When HIV appeared and began to cause immunodeficiency, this was the first time that this type of virus caused such a disease. Before that, we only knew about retroviruses from studies of gamma retroviruses that cause cancer. Retroviruses are types of viruses that can be considered as viruses traveling light. For example, HIV has only nine genes, and other retroviruses have three in general. So they really travel light compared to the herpes virus, for example, which has about two hundred genes. I think their strategy is to travel light and be quiet. Their goal when a cell is damaged is not to activate it and not cause much damage. I think that initially they do not cause severe diseases, but in the long term this infection can cause diseases like cancer in mice. Although, perhaps, they will not cause cancer in wild mice. This happens only when we break through the mouse protection.
So, retroviruses are relatively merciful viruses, I believe, because they don't control your body like other viruses do. Their main difference is that they convert RNA into DNA and integrate DNA into chromatin. This is a unique feature of retroviruses. Some other viruses do the same, but only as a supplement. Retroviruses depend entirely on this integration process. If a cell cannot get rid of them, it must die to rid itself of a viral infection.
Retroviruses insert their genome into the host chromatin. Once these genes get inside the chromatin, they will stay there forever. The cell as a whole treats them as cellular genes, so they are read, produce RNA, and later this RNA is sent to the cytoplasm. The virus produces protein, the cell produces viral protein, new viruses are formed, and they are ready to move on, infect new cells. So retroviruses have become a great tool for studying cell biology, and that's because they're simple. Some of them have only three genes. Even a complex retrovirus like HIV has only nine genes. Therefore, it is very easy to take them, divide them into parts and study which part is responsible for what.
In the field of gene therapy, there is a trick when they take a retrovirus, take the retroviral genes out of it and insert the genes that are needed. Then retroviral particles can be formed. This trick can be used to develop a retroviral vector. It works like this: you can take a retroviral genome, which usually encrypts all retroviral genes, get rid of them and put in their place a preferred gene, for example, a therapeutic gene or a gene that can be simply measured – we usually use GFP, which makes cells turn green. If you do this, you will be able to produce retroviral particles that will only infect the cell and produce protein. There will be no retroviral genes in the retrovirus, so it will only be able to produce therapeutic genes or ZFB. And it's a great tool for studying cell biology.
For example, you can change a cell and see if the virus continues to exert its influence on it, or you can, on the contrary, change the virus and check whether it can now infect the cell. This will be called the genetic approach. It is possible to find out the role of various parts of the virus in getting into the cell nucleus, in getting into the cell, in crossing the cytoplasm.
In addition, we can use retroviral vectors to study cell biology. We can use them to make cells produce a specific gene by referring to the process of RNA interference. You can use retroviruses to produce RNA interference, you can use retroviruses to isolate a specific gene. The most common use of retroviruses lately is to deliver CRISPR/Cas9, so that we can eject any gene in a particular cell, and then study the consequences of this "ejection" or measure anything like cell division, their growth, or anything related to cells.
Many laboratories focus on research on retroviral vectors and retroviruses to study innate immunity. Innate immunity, or intracellular innate immunity, is the ability of an individual cell to protect itself from a viral infection. I think this is quite an exciting direction. The realization of its importance happened not so long ago, about 20 years ago. Now we understand that we are under the attack of viral infections throughout evolution. During this time, we have developed very complex ways to protect ourselves from infections. We have an adaptive immune system, T-lymphocytes and antibodies. But besides that, every cell in our body has the ability to protect itself from infection. Retroviruses provide an excellent opportunity to study this.
For example, we are trying to find out how a cell understands that a virus has got inside it. She does this through a process we call pattern recognition. There are molecules in our cells that can detect an incoming virus because they notice something that looks different from a conformational and chemical perspective. If the pattern recognition receptor sees an incoming virus, it will trigger an antivirus response. A few things will start happening. First of all, the cell will begin to produce much more protein than it did before. It also begins to secrete a protein of the type interferon type 1, which will allow uninfected cells to know that a virus is approaching. Interferons activate these uninfected cells to produce their antiviral protection. This is a fantastically effective way to resist viral replication. Since retroviruses with their three and nine genes are very simple, we can produce mutations and observe whether they are still able to pass through protection, and we can understand exactly how they do it.
About the author:
Greg Towers – Professor of Molecular Virology, University College London; Head of Research Group, UCL Division of Infection and Immunity.
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11.09.2017