Genome Variability: Videos & Practice Problems

Genome variability arises from differences in DNA sequences among strains of a species, characterized by the pangenome, which includes all genes across strains, and the conserved genome, or core genome, which consists of shared genes. Mobile genetic elements (MGEs) like plasmids, transposons, genomic islands, and phage DNA contribute significantly to this variability. Plasmids can carry antibiotic resistance genes, while transposons can alter gene locations, potentially leading to insertional inactivation. Genomic islands, often acquired through horizontal gene transfer, can contain pathogenicity genes, enhancing a bacterium's ability to cause disease.

Genome Variability

In this video, we're going to begin our lesson on genome variability. Scientists have discovered over the years that different strains of a single species can have some genome variability. In other words, different strains of a single species can have some differences in their genome or their DNA sequences. Now, in order to better understand this genome variability, we need to introduce these two terms that you see down below. The genome of all strains within a species is composed of 2 elements. The first element is called the pangenome, and the second element is called the conserved genome, or in other words, the core genome.

The pangenome refers to all of the genes in every strain of the species. This includes the genes that are unique across different strains as well as the genes that are consistent across different strains. The pangenome refers to all of the genes in every strain of a species. On the other hand, the conserved genome or the core genome does not refer to all of the genes. Instead, it only refers to the genes that are conserved, shared, or consistent across every strain of that species.

In order to better understand these two terms, we have this image down below. This image represents the pangenome of a specific species that has 3 different strains. Strain number 1 is represented by this green circle. Strain number 2 is represented by a blue circle. And then strain number 3 is represented by a pink circle. These are 3 different strains of the same species. When we're collectively looking at all of the genes in every strain of the species, we're looking at the pangenome. This here represents the pangenome; the genes of strain 1, strain 2, and strain 3.

The core genome, the conserved or core genome, only refers to the genes that are conserved, shared, or consistent. In this image, the core genome is represented right here within the shaded area because there's overlap between all three strains. This can be labeled as the conserved genes, otherwise known as the core genome. As we can see, the conserved genome is always going to be consistent across every strain of that species, but each strain will also have unique genes. This here concludes our brief introduction to genome variability.

As we move forward in our course, we're going to talk about some of the elements that contribute to genome variability. I'll see you all in our next video.

Genome Variability

In this video, we're going to introduce our mobile genetic elements map. The variability between genomes of different strains of the same species is significantly attributed to what scientists call mobile genetic elements. Mobile genetic elements are sometimes abbreviated as MGEs for short. These mobile genetic elements or MGEs are really just segments of DNA that can move, as is implied by the term mobile, which means move. These are segments of DNA that can move from one DNA molecule to another. Some examples of mobile genetic elements include plasmids, transposons, genomic islands, and phage DNA. Moving forward in our course, we're going to talk briefly about each of these different mobile genetic elements in their own individual videos.

What you'll notice is down below, we're showing you our map of the lesson on mobile genetic elements or MGEs. On the far left over here, we're going to talk about plasmids. Then, here we're going to introduce what are known as transposons. Then over there, we're going to introduce what are called genomic islands. And last but not least, on the far right, we're going to revisit phages and phage DNA. This does represent a map of our lesson, and you can use it to help guide you as we move forward in the course.

As always, we're going to be covering the map by following the leftmost branch first and then zooming out and covering each of these topics in that particular order. I'll see you all in our next lesson video to talk more about plasmids.

Plasmids

In this video, we're going to focus on plasmids. Plasmids can be defined as circular double-stranded DNA molecules with an origin of replication, allowing them to replicate within a cell. Some plasmids are known as high copy number plasmids, and these are plasmids that replicate very fast or quickly inside of a cell. Other plasmids are known as low copy number plasmids, and so they replicate very slowly within the cell. These high copy number plasmids that replicate quickly, of course, are going to be found in high numbers or high copy number because they replicate so fast. Whereas, the low copy number plasmids that replicate slowly are going to be found in relatively low numbers within the cell or low copy number. These plasmids, regardless of if they are high copy number or low copy number plasmids, can carry various genes. Sometimes, some of those genes are going to be able to provide the cell with the ability to survive in a particular environment, such as an environment that contains antibiotics, for example. We call these plasmids resistance plasmids, otherwise known as r plasmids. Resistance plasmids or r plasmids are plasmids that encode genes that confer resistance to antibiotics, allowing the cell to survive in the presence of antibiotics. These genes, found on the resistance plasmids, are sometimes referred to as R genes.

In addition to the R genes, it's important to note that these plasmids can also have other genes. Most resistance plasmids are going to be conjugative plasmids, which means that these plasmids can be horizontally transferred between different species via conjugation. Aside from the R genes, they can also contain other genes that are required for DNA transfer by conjugation.

If we take a look at our image down below over here on the left-hand side, notice that the top half of this image is focusing on high copy number plasmids. High copy number plasmids, you'll notice, replicate very quickly within the cell, and so they're going to be found in relatively high numbers, high copy numbers, within the cell. Whereas the low copy number plasmids on the bottom half over here, notice that they replicate very slowly over time, and so they're going to be found in relatively low numbers within the cell.

Now over here is a representation of a plasmid and some of the different regions of DNA that can be found within the plasmid. What you'll notice is that it contains an origin of replication, allowing it to replicate, and this is specifically an r plasmid here, a resistance plasmid. It's a resistance plasmid because it contains specific genes that allow for antibiotic resistance, such as an amp_R gene, which allows for ampicillin resistance, a gene that allows for ampicillin resistance, allowing the cell to survive in the presence of ampicillin. Up at the top is a gene, the tet_R gene or for tetracycline resistance. Resistance to yet another antibiotic. And then over here in purple, what we have is a CAN_R gene providing resistance to an antibiotic called kanamycin. And in addition to being our plasmid, it's also a conjugated plasmid as well because it contains this tra region or tra region here, which is the region that is important for conjugation, allowing the r plasmid to be horizontally transferred and passed from cell to cell via conjugation. This also allows for the spreading of resistance genes as you see here between different species of bacteria.

This concludes our brief lesson on plasmids and how they contribute to genome variability because they are mobile genetic elements that can be passed from one cell to another cell via conjugation. We'll be able to talk about other mobile genetic elements as we move forward in our course, so I'll see you all in our next video.

Transposons in Prokaryotes

In this video, we're going to introduce transposons. Transposons are also sometimes referred to as jumping genes. Transposons or jumping genes refer to pieces of DNA that have the ability to alter or change their locations within a cell's genome. Transposons are able to alter their locations within a cell's genome through a process known as transposition. Transposition is the name of the process that allows transposons to alter their locations within a cell's genome. It is the process of the movement of a transposon to a different location within the cell's genome. Transposons, being pieces of DNA, encode for a protein, specifically an enzyme known as transposase. Anything that ends in -ase is an indication that it is an enzyme. Transposase is an enzyme that catalyzes transposition, allowing the transposon to move to different locations within the cell's genome. Sometimes, transposition can lead to what is known as insertional inactivation. Insertional inactivation occurs when the gene that a transposon jumps into or gets inserted into becomes inactivated. We can get a better understanding of transposons, transposition, and insertional inactivation as we look at our image down below.

Notice that this is an image of transposons or jumping genes. On the left-hand side, we're showing you a bacterial cell, and you can see in blue it represents the bacterial chromosome. The little green region on the left of the chromosome represents the transposon. Over on the left, you have the little yellow region of the chromosome, which refers to gene X, just another gene within the cell. Zooming into this specific region, this part of the diagram depicts the transposon's capability for transposition, meaning it can change its location within the cell's genome. The starting position is over on the left-hand side of the chromosome. However, the transposon, also known as a jumping gene, can change its location and insert itself into a different region within the chromosome. Just like this frog here can jump into a different location, the transposon can jump into a different region. Gene X, as shown in this image, is active. However, after transposition occurs, after the movement of the transposon, it could possibly lead to insertional inactivation. This is when the transposon inserts itself into a gene and inactivates it. The transposon's ending position, which is over here on the right, is inserted into gene X and, therefore, disrupts and inactivates gene X. Transposons can help to create genetic variability and, in some cases, lead to insertional inactivation, thereby inactivating specific genes.

This here concludes our brief lesson on transposons, transposition, and insertional inactivation. We'll be able to get some practice applying these concepts and learn about other mobile genetic elements as we move forward in our course. So I'll see you all in our next video.

Transposons encode the enzyme _________ which catalyzes the insertion of the transposon.

• A. DNA glycosylase.
• B. Excisionase.
• C. Transposase.
• D. DNA polymerase.
• E. Integrase.

Answer: (C)

Genomic Islands

In this video, we're going to briefly introduce genomic islands. Genomic islands refer to relatively large regions of a bacterium's chromosome that are believed to have originated in a different species. This bacterium would have obtained the genomic island through some form of horizontal gene transfer. Scientists can identify these genomic islands because they have a unique ratio of GC base pairs. Recall that G's and C's refer to the nitrogenous bases or the sequence of the DNA. These GC base pairs have unique ratios within different species. Therefore, the genomic island will have a unique GC ratio that is different from the rest of the cell's chromosome, which has a different GC ratio.

Pathogenicity islands are specific types of genomic islands that contain genes giving the cell the ability to cause disease. Anything that is a pathogen is an agent capable of causing disease. If we take a look at our image below, you'll notice that it shows a bacterial cell and within the bacterial cell, you have the bacterium's genome. Its chromosome here is colored into two different regions. It has this relatively large region which is going to be the genomic island, specifically a pathogenicity island, a specific type of genomic island that makes the cell pathogenic allowing it to cause disease. You'll notice that the pathogenicity island has a specific ratio of GC base pairs that differs from the GC ratio of the rest of the cell's chromosome. This pathogenicity island somewhat seems like a little island in the middle of an ocean, if you will. This is somewhat why they might be called genomic islands because they somewhat appear to be like a little island here surrounded by DNA sequences that have different GC ratios.

This here concludes our brief introduction to genomic islands, and we'll be able to get a little bit of practice on these concepts as we move forward and then talk about phages as the last mobile genetic element. So I'll see you all there.

Which of the following answers about genomic islands is a true statement?

• A. Genomic islands create genetic variability within a species.
• B. Genomic islands originated from a different species than the one they currently reside in.
• C. Genomic islands can hold pathogenic genes which allows the bacteria they reside in to cause disease.
• D. All of the above are true statements about genomic islands.

Answer: (D)

Phage DNA

In this video, we're going to talk about phage DNA as a mobile genetic element. First, we need to recall from our previous lesson videos that phages or bacteriophages are particles of DNA or RNA surrounded by a protein coat. These phages serve as viruses that infect bacteria. Also recall from our previous lesson videos that certain types of phages are capable of inserting their DNA into the host cell's chromosome, creating what scientists call a prophage. The prophage can be replicated along with the remainder of the chromosome, and therefore the prophage can be passed on to the progeny of the cells or to the offspring of the cells. Phage DNA is a mobile genetic element because it's capable of moving and being transferred to different organisms. What you'll see here in this image is a phage, infecting a bacterial cell and injecting its genetic material, injecting the phage DNA. The phage DNA can then, of course, integrate into the host cell's chromosome to create a prophage, as we see over here. Once the prophage, the viral DNA here is integrated, it can then be replicated and passed down as this cell replicates and divides. This is a mobile genetic element that can essentially be transferred between different organisms and passed down. This here concludes our brief lesson on phage DNA as a mobile genetic element, and we'll be able to get some practice applying these concepts as we move forward. So, I'll see you all in our next video.

Here’s what students ask on this topic:

What is genome variability and why is it important?

Genome variability refers to the differences in DNA sequences among different strains of a single species. This variability is crucial because it allows for adaptation and survival in changing environments. For example, some strains may develop resistance to antibiotics, giving them a survival advantage. Genome variability is characterized by the pangenome, which includes all genes across strains, and the conserved genome, or core genome, which consists of shared genes. Understanding genome variability helps scientists develop better treatments for diseases and understand the mechanisms of evolution and adaptation.

What are mobile genetic elements and how do they contribute to genome variability?

Mobile genetic elements (MGEs) are segments of DNA that can move from one location to another within a genome or between genomes. Examples include plasmids, transposons, genomic islands, and phage DNA. MGEs contribute to genome variability by introducing new genes or altering existing ones. For instance, plasmids can carry antibiotic resistance genes, while transposons can change their location within the genome, potentially inactivating other genes. Genomic islands, often acquired through horizontal gene transfer, can contain genes that enhance a bacterium's ability to cause disease. These elements play a significant role in the evolution and adaptability of organisms.

What is the difference between the pangenome and the core genome?

The pangenome encompasses all the genes present in every strain of a species, including both unique and shared genes. In contrast, the core genome, also known as the conserved genome, consists only of the genes that are consistent and shared across all strains of the species. The pangenome provides a comprehensive view of the genetic diversity within a species, while the core genome highlights the essential genes necessary for the basic functions and survival of the species. Understanding both concepts is crucial for studying genome variability and the evolutionary dynamics of species.

How do plasmids contribute to antibiotic resistance?

Plasmids are circular double-stranded DNA molecules that can replicate independently within a cell. Some plasmids, known as resistance plasmids or R plasmids, carry genes that confer resistance to antibiotics. These genes, called R genes, enable the host cell to survive in the presence of specific antibiotics. Plasmids can be transferred between bacteria through a process called conjugation, spreading antibiotic resistance genes across different species. This horizontal gene transfer is a significant factor in the rapid spread of antibiotic resistance, posing a challenge for treating bacterial infections effectively.

What are transposons and how do they affect the genome?

Transposons, also known as jumping genes, are pieces of DNA that can change their location within a genome through a process called transposition. Transposons encode an enzyme called transposase, which facilitates their movement. This movement can disrupt genes at the insertion site, leading to insertional inactivation. By altering gene locations, transposons contribute to genome variability and can impact gene expression and function. In some cases, transposons can introduce new genetic material or regulatory elements, influencing the evolution and adaptability of organisms.