Transposons and Viruses - Online Tutor, Practice Problems & Exam Prep

Mobile genetic elements, including DNA transposons and retrotransposons, play a crucial role in genome evolution by causing mutations through their movement within the genome. DNA transposons utilize a cut-and-paste mechanism, while retrotransposons reverse transcribe RNA back into DNA for insertion. These elements can disrupt genes or regulatory sequences, influencing traits such as antibiotic resistance in bacteria and genetic diseases like hemophilia in humans. Their activity contributes significantly to genetic diversity and evolution, with varying frequencies of movement across different organisms.

Mobile Genetic Elements

Hi, in this topic, we're going to be talking about transposons and viruses. So the first thing we're going to talk about is mobile genetic elements, which are defined as "jumping genes." These are small DNA segments that are found in every single cell. And so, what they do is they actually insert themselves into any DNA sequence within a cell, but they cannot leave. So it's not like they can reproduce themselves and jump between cells. They're stuck in a single cell, but within that cell, they can jump all over the place within the genome. Surprisingly, they make up a fairly large proportion of the genome, about 50%. And, even more surprisingly, they really have no function. People call them selfish genes because they don't do anything other than just copy themselves and insert into the genome. They can insert anywhere they want: in certain genes, in regulatory sequences, in centromeres, and telomeres, and any chromosome.

So, who discovered these? This is a name you're going to want to know: Barbara McClintock. She was actually studying corn. You may see this as maize, for all you non-farmers out there, that's just the type of corn. She discovered them in the 1940s. She was really instrumental in finding these, and that's probably a name that you may be quizzed about in the future.

Since then, we've found that there are really two types. There are DNA transposons, your mobile genetic elements, and retrotransposons, which instead of using DNA, use RNA. These are the two major families of mobile genetic elements. Now, another type of mobile genetic element that you may hear about is actually viral genomes, especially retroviral genomes. Retroviral genomes are very similar to retrotransposons; they use RNA. We'll talk about them more in different topics, but viral genomes can actually insert themselves into the genome in very similar ways that mobile genetic elements do, and they have the ability to, sometimes, occasionally move around, especially when they're first infecting the cell. They can insert themselves in the genome kind of anywhere they want.

So if we just look at this example here, let me move out of the way. You can see here there’s a transposon and a gene, and that transposon can move and insert itself into the gene. Now, it doesn't always have to insert itself into the gene; it could have inserted itself here or there. It kind of can insert anywhere, but sometimes they do insert into genes, and that can cause some serious effects. So now, let's move on.

DNA Transposons

So, in this video, we're going to talk about DNA transposons, which is one of the types of mobile genetic elements. Like I said, a type of mobile genetic element. And they actually move through a DNA intermediate, surprisingly enough. These are most commonly found in prokaryotes and bacteria mainly because the eukaryotic DNA transposons have generally lost their ability to move, so they no longer move anymore. However, remnants of them still exist in the human genome. So, about 3% of the human genome is just DNA transposons that really have no function now because they can't move.

And so, how do DNA transposons move in the genome? Well, it's kind of just like cut and paste. They're cut from one region and pasted into another. One of the side effects of this is that if it's actually cut during DNA replication, then it can duplicate because it's already being replicated. Then, if you replicate it and then cut it, it's going to insert into a new region of the genome, which, when it's replicated again, will just be copied twice.

So, what's the structure of the DNA Transposon? It contains this very unique structure and has inverted repeats of 50 base pairs. Those are just repeated sequences on either end of the transposon, and the middle of the transposon sequence actually encodes for a gene that codes for protein and that protein is a transposase. So, what is the transposase? The transposase is responsible for cutting or removing the transposon out of the DNA sequence. So the transposase is kind of your scissors for the DNA transposon. And one of the really important aspects of this is we think, cut and paste, cut and paste, there are scissors there chopping things up. But this is important because it doesn't lose length when it inserts or when it cuts. And so, because it isn't losing length, it's still able to continue this cut and paste pretty much indefinitely throughout the lifetime of the cell.

And so, the transposase is responsible for cutting. But what's responsible for pasting? And that's actually this process called double-strand break repair which you may have heard of. You don't necessarily need to know that term right now; we'll talk about it more in other topics. But if the transposase is the cause, then the transposase is the scissor, then the double-strand break repair is the glue that sort of pastes it back together. So, if we're looking at a structure of a DNA transposon, it has these inverted repeats on either side. And this is a protein-coding region. And what does this encode for? This encodes for transposase, and that's kind of the scissors that can cut it out of its genomic location so that it can move to a different location.

So now let's move on.

Retrotransposons

Okay. So in this video we're going to talk about retrotransposons. These are, again, mobile genetic elements. But instead of moving through DNA, they move through an RNA intermediate. So how does this happen? Well, while they're in the genome, they are of course in DNA chromosomes which have DNA. So they have to be in DNA. What happens is that they are actually transcribed into RNA and then processed back into DNA to insert. The enzyme responsible for taking RNA and sort of reverse transcribing it back into DNA is called reverse transcriptase. The process of changing is actually called reverse transcribing, and that moves RNA to DNA. It's different than transcribing which uses DNA to RNA. If we were to look at what this looks like, you have your DNA sequence here. There's a retrotransposon, which, remember, is in DNA form. It is then transcribed, and a portion of it is translated. This allows for different complexes to form. You don't really need to know about this but eventually, it undergoes reverse transcription. So it changes from this RNA here back into DNA, and that DNA can then integrate right here into the genome in a new location. So that's kind of how retrotransposons work.

Now, there are a couple of different classes of retrotransposons. The first one that I'm going to talk about are long terminal repeat retrotransposons. They make up about 8% of the human genome. They're called long terminal repeats because they have long terminal repeats. These direct repeats are about 200 to 600 base pairs long. Like the DNA transposon, they actually flank a protein-coding region. The second class are the non-long terminal repeat retrotransposons. There are two types of these. One of them is called LINEs, which stands for Long Interspersed Elements. LINEs are not commonly found in mammals and are about six kilobases long, hence the name 'long'. There are three classes, LINE-1, LINE-2, and LINE-3, but only LINE-1 is still functional. They actually make up a large portion of the human genome, about 21%. This is surprising because they are not commonly found in mammals but are still present in large amounts in the human genome. Most of these do not move; they are kind of dead. They just sort of sit there and cannot move anymore but they do still exist.

The second kind, like the other transposons that we've talked about, can take repeats followed by a protein-coding region in the center. The second class is the short interspersed elements or SINEs for short. These are commonly found in mammals. They are called short because they are about 300 base pairs long, much shorter than the six kilobases you see in the long interspersed repeats. The most common is the ALU element, and this one is actively transposing in the human genome. When you look at it, this can still happen, moving around in the genome. SINEs make up about 13% of the human genome, with 10% of it actually being ALU elements. These are a little different than the other transposons because most of them lack a protein-coding region and instead depend on the presence of other mobile elements like LINEs or long terminal repeat retrotransposons, or even DNA transposons to provide things like transposases and other proteins necessary for their jumping. So, it's a little unusual because they are still present but do not have everything they need to jump, so they depend on these other elements to jump but they are still one of the most actively moving mobile elements in the human genome. ALU is quite significant. Very much like you've seen in some of these other images that I've been showing you, the structure of a LINE, it has these repeats here on the end. That's actually a repeat. You don't actually need to know what this is, so ignore that. But it has these two protein-coding regions right in the center, which is very similar to these other transposons that we've talked about. So now let's move on.

Viruses as Mobile Genetic Elements

Okay. So far we've talked about different kinds of DNA elements that can actually jump around the genome, but viruses can do that as well. And so, viruses act as mobile genetic elements, and this is because some viruses can actually integrate their genome into the cell they infect or the host cell. Let's talk a little bit about the virus structure, and then we can go into how they act and how they actually integrate and can jump around through the genome. Viruses are really simple types of things. They just contain a protein coat that surrounds some type of genetic information. The amount of genetic information is just really small compared to other living organisms, and this genetic information can be either DNA or RNA-based. Generally, we are familiar with viruses because they cause disease, but they are also very useful tools in a laboratory setting, and so they can do more than just cause disease.

Now, there are different types of viruses, of course, depending on how they infect, what kind of genetic material they have. One really important type that we've mentioned before are bacteriophages, and these are viruses that infect bacteria. These can insert their genome into the host bacteria that they've infected. And when they insert their genome, that genome just gets inserted anywhere. There's not usually a very specific sequence, and so it can be in a gene, in a regulatory sequence, or nowhere important, but where it inserts can have a drastic impact on the organism itself. There are retroviruses, and this is a really important class that we're going to talk a lot about. Retroviruses are called that because they have RNA as their genetic material and not DNA, and they use their RNA as a template to produce DNA. So they start with RNA, it's just this template, and that is, in a process called reverse transcription, to actually transcribe it into DNA. And because it's called reverse transcription, the enzyme that does that is called reverse transcriptase. And, this enzyme is not really found in humans, or in the host cell for the most part but is instead encoded by the virus itself. So the virus contains this gene for reverse transcriptase, and that is what allows the virus to reverse transcribe that RNA and use it as a template to produce DNA.

Here's just a structure of a retrovirus. It's not super important that you understand and be able to label this yourself, but the important thing here is that there's just this protein coat that is surrounding this genetic material. And because it's a retrovirus, we know that it's going to be RNA, not DNA. So here's this RNA here. And, when this virus is to infect something, whatever it infects, then that RNA will be used to reverse transcribe into DNA. Now, the viral genome is generally integrated into the host genome, and that's why we say these act as mobile genetic elements. Right? Because it has its own RNA or DNA that is actually just inserted into the genome wherever it pleases. So it's actually this mobile genetic element that can jump around different places depending on where it's inserted at the moment the virus infects. Now, in order to insert, it has to have some type of enzyme that's going to actually insert it, very similarly to all the other types we've talked about. And this enzyme for viruses is integrase, which makes sense. Aces is the enzyme, and then integrase is for its being integrated. It makes complete sense.

And so, this inserts the viral DNA into the host genome. Now remember, this is DNA not RNA because if the virus has RNA, that's going to be used as a template to produce DNA before it's integrated. So DNA is always integrated. RNA is not going to be integrated into the genome. Here's an example of the HIV genome and how it integrates into the host cell DNA. Now, of course, there's a lot of information here, like CCR4 receptor. None of this stuff you need to know. Just know here's the virus and here it is infecting a cell. And you can see that it has this DNA or has RNA, it's HIV, it's inside, and then reverse transcriptase comes in and synthesizes it into DNA. So here we now have DNA, which is here. This gets into the cell nucleus, and here's the viral DNA in this dark black. And you can see that it integrates into the host cell genome where the dark black is here, that's the virus, and the lighter color is just the host cell. And so this is very common among especially retroviruses. It can be done through other viruses as well, but retroviruses, this is a really common process. And that's why we say viruses can act as mobile genetic elements as well. So with that, let's now move on.

Evolution

So in this video, we're talking about mobile genetic elements and their role in evolution. Because mobile genetic elements are jumping all the time, you can very much imagine how they're playing this major role in evolution because each time they jump they're disrupting the genome. This is causing some kind of mutation, whether it's a shift of a gene or inserting into a gene; these mutations can have huge effects on evolution. How often do these things jump? You might wonder if they are jumping every second or once every 10,000 individuals. Well, that depends on the organism. For bacteria, this occurs once every \(10^5\) cell divisions, which for bacteria is actually fairly often. It does not happen in every cell, but after all these divisions, which happen fairly rapidly, it does occur. This is actually an example of something we hear a lot about in the news: antibiotic resistance, often conferred through mobile genetic elements. A gene that allows the bacteria to survive or a gene that deals with the antibiotic is affected by a mobile genetic element jump.

For fruit flies, 50% of their spontaneous mutations occur from mobile genetic elements. For mice, this is significant, about 10% of total mouse mutations in the current mouse genome are due to mobile genetic elements. For humans, this happens much less, one in every 1,000 mutations, which are fairly rare anyway, contributing to about 0.1 to 0.2% of all mutations. There has been one interesting example of a mobile genetic element causing a disease, hemophilia, in a patient with no family history of it. Hemophilia is usually a genetic disease that is passed on in families, but this person developed it because a mobile genetic element had jumped into the disease gene causing hemophilia.

Mobile genetic elements can have effects larger than just the gene itself jumping; sometimes, when they move, they can carry adjacent regions of the genome with them. Thus, they could be moving regulatory regions or certain exons of a gene to different places in the genome. Throughout evolution, there have been some really important mobile genetic element jumps that have led to life as we know it today. Some important proteins that arose from mobile genetic elements include transcription factors, which are crucial in controlling gene expression, and telomerase, an enzyme vital for maintaining telomeres. You don't necessarily need to know these terms now; we'll talk about them in future lessons, but just understand that some important proteins have come from mobile genetic elements—so not all of them are bad.

Finally, in terms of mobile genetic elements and evolution, they affect the expression of genes and proteins and can be inherited. If mobile genetic elements are in the germ cells and they jump, that will be passed on to offspring. So, that's mobile genetic elements and evolution. Now, let's move on.

Which of the following is not considered a mobile genetic element?

• A. DNA transposons
• B. SINEs
• C. Transposase
• D. Retrotransposons

Which of the following transposons still jumps in the human genome?

• A. L1 LINE
• B. L2 LINE
• C. L3 LINE

What is the name of the enzyme responsible for allowing the transposon to jump within the genome?

• A. Reverse Transcriptase
• B. Transposase
• C. Transposonase
• D. Integrase

Some transposons encode for a protein.

• A. True
• B. False

Here’s what students ask on this topic:

What are transposons and how do they function in the genome?

Transposons, also known as jumping genes, are mobile genetic elements that can move within a genome. They are segments of DNA that can insert themselves into various locations within a cell's DNA. There are two main types: DNA transposons and retrotransposons. DNA transposons use a cut-and-paste mechanism, where they are cut from one location and inserted into another. Retrotransposons, on the other hand, move via an RNA intermediate. They are transcribed into RNA, which is then reverse transcribed back into DNA by the enzyme reverse transcriptase before being inserted into a new location. This movement can disrupt genes or regulatory sequences, leading to mutations and contributing to genetic diversity and evolution.

Who discovered transposons and what was the significance of this discovery?

Transposons were discovered by Barbara McClintock in the 1940s while she was studying maize (corn). Her groundbreaking work revealed that certain DNA segments could move within the genome, a concept that was revolutionary at the time. This discovery was significant because it challenged the prevailing view of the genome as a static entity and introduced the idea that genetic elements could be dynamic. McClintock's work laid the foundation for understanding genetic regulation and mutation, and she was awarded the Nobel Prize in Physiology or Medicine in 1983 for her contributions to the field.

How do retrotransposons differ from DNA transposons?

Retrotransposons and DNA transposons are both types of mobile genetic elements, but they differ in their mechanisms of movement. DNA transposons move through a cut-and-paste mechanism, where they are excised from one location in the genome and inserted into another. This process is facilitated by the enzyme transposase. Retrotransposons, on the other hand, move via an RNA intermediate. They are first transcribed into RNA, which is then reverse transcribed back into DNA by the enzyme reverse transcriptase. The newly synthesized DNA is then inserted into a new location in the genome. This difference in mechanisms means that retrotransposons can increase their copy number within the genome, while DNA transposons typically do not.

What role do mobile genetic elements play in evolution?

Mobile genetic elements, such as transposons, play a significant role in evolution by introducing genetic diversity. Their ability to move within the genome can cause mutations by disrupting genes or regulatory sequences. These mutations can lead to new traits or variations that may be subject to natural selection. For example, in bacteria, mobile genetic elements can confer antibiotic resistance, providing a survival advantage. In higher organisms, they can contribute to genetic diseases or beneficial adaptations. Over evolutionary time, the activity of mobile genetic elements has shaped genomes, influencing gene expression, genome structure, and the emergence of new genes.

How do viruses act as mobile genetic elements?

Viruses can act as mobile genetic elements by integrating their genetic material into the host genome. This is particularly true for retroviruses, which have RNA genomes. Upon infecting a host cell, the viral RNA is reverse transcribed into DNA by the enzyme reverse transcriptase. The newly synthesized viral DNA is then integrated into the host genome by the enzyme integrase. Once integrated, the viral DNA can be transcribed and translated by the host's cellular machinery, producing new viral particles. This integration can disrupt host genes or regulatory sequences, leading to mutations and potentially altering the host's genetic makeup.