Absorbing DNA

[Resha Caner]

The Bacteria That Steals DNA

Horizontal Gene Transfer (HGT) is nothing new, but I've always thought of it as an accidental occurrence rather than a directed one. So I have some questions about Streptococcus pneumoniae upon which maybe our resident biologists can shed some light.

1) What is the success rate for absorbing DNA? Do the bacterial organisms absorb DNA from their hosts 100% of the time, 1%, 0.01%?
2) What amount of DNA do the bacterial organisms absorb? 100% of the host DNA, 1%, 0.01%?
3) Do the bacterial organisms appear to target specific regions of their host DNA, or is it random?

Answering some of those questions may require helping me to understand the mechanism. And, as always, I realize no one is obligated to help me, so I just appreciate whatever can be offered.

 

[Mike Lane]

The Bacteria That Steals DNA

Horizontal Gene Transfer (HGT) is nothing new, but I've always thought of it as an accidental occurrence rather than a directed one. So I have some questions about Streptococcus pneumoniae upon which maybe our resident biologists can shed some light.

1) What is the success rate for absorbing DNA? Do the bacterial organisms absorb DNA from their hosts 100% of the time, 1%, 0.01%?
2) What amount of DNA do the bacterial organisms absorb? 100% of the host DNA, 1%, 0.01%?
3) Do the bacterial organisms appear to target specific regions of their host DNA, or is it random?

Answering some of those questions may require helping me to understand the mechanism. And, as always, I realize no one is obligated to help me, so I just appreciate whatever can be offered.

Here is a list of books & papers you can read:
Horizontal Gene Transfer - Google Scholar

Why do you need someone to explain it to you?

 

[Bugeyedcreepy]

...Why do you need someone to explain it to you?

Don't really, it is convenient though that there are biologists and scientists here that are Excellent at concisely explaining the terms and concepts in such a way that even laypeople like myself learn these valuable tidbits of science. Besides, this is an incredibly appropriate place to glean this info - many people here would benefit from it, wouldn't you agree?

 

[PsychoSarah]

The Bacteria That Steals DNA

I'm made wary by the fact that this article sites no sources. It also is prone to some poor wording.

1) What is the success rate for absorbing DNA? Do the bacterial organisms absorb DNA from their hosts 100% of the time, 1%, 0.01%?

They don't absorb it from their hosts, but from other bacteria, typically from members of the same species. Absorb is also a poor word choice, transfer is far better.

2) What amount of DNA do the bacterial organisms absorb? 100% of the host DNA, 1%, 0.01%?

Pretty small portions, though it varies depending on the mechanism. Bacterial conjugation (which is the closest thing bacteria have to sexual reproduction) probably contributes the most change in a single instance compared to the other methods, which are just a few genes. So, generally far less than 0.01%, but due to variation, I can't really quantify it into a specific number.

3) Do the bacterial organisms appear to target specific regions of their host DNA, or is it random?

Well, in conjugation, specific regions do seem to be targeted, though not all carry useful genes, some being comparatively "parasitic" in the sense that they just waste resources during replication. It can be completely random in some methods of horizontal gene transfer.

Answering some of those questions may require helping me to understand the mechanism. And, as always, I realize no one is obligated to help me, so I just appreciate whatever can be offered.

I think your issue is that it isn't just 1 mechanism. There's:
1. Transformation
2. Transduction
3. Bacterial conjugation
as the mechanisms by which genes can be transferred from one bacterium to another. Viruses and virus-like agents can also do it. Genes aren't usually just floating around for a bacteria to take up and integrate into their own biological makeup.

What's scarier is that viruses can also do it to us, hence why certain cancers are connected with specific viral infections.

 

[Resha Caner]

I'm made wary by the fact that this article sites no sources. It also is prone to some poor wording.

First, thanks for the content you provided in your reply. Second, I was aware the article was pop science when I referenced it. It was just a place to start the conversation. The problem is I'm not confident in my ability to interpret more technical sources, and I didn't want the conversation to take some unintended left turn.

They don't absorb it from their hosts, but from other bacteria, typically from members of the same species. Absorb is also a poor word choice, transfer is far better.

I was able to find published papers from Dr. Håvarstein (who was mentioned in the first article), but the topic was just as you said, involving transfers between bacteria. Maybe, then, this article is closer to my interest.

Finally, I know viruses insert themselves into human DNA, but my interest was more the other way round. Do they ever take DNA from humans? I couldn't tell from your reply if you were saying they do.

 

[PsychoSarah]

First, thanks for the content you provided in your reply. Second, I was aware the article was pop science when I referenced it. It was just a place to start the conversation. The problem is I'm not confident in my ability to interpret more technical sources, and I didn't want the conversation to take some unintended left turn.



I was able to find published papers from Dr. Håvarstein (who was mentioned in the first article), but the topic was just as you said, involving transfers between bacteria. Maybe, then, this article is closer to my interest.

Finally, I know viruses insert themselves into human DNA, but my interest was more the other way round. Do they ever take DNA from humans? I couldn't tell from your reply if you were saying they do.

Viruses don't take DNA from those they infect to use themselves. However, it is not uncommon for them to take surface proteins from infected cells to "hide" from the immune system and camouflage as a native cell.

When the viral DNA/RNA inserted into a cell commands the cell to make more of it, if it inserts itself into the DNA to do so, nearby genes native to the cell can get copied along with the virus and "tag along for the ride", so to speak. Thus, when the new viruses infect a host cell of the same species (and sometimes different but similar species), they transmit the gene with them.

That article is probably closer to your interest, but also isn't particularly credible.

 

[Resha Caner]

That article is probably closer to your interest, but also isn't particularly credible.

Again, I was only looking for indicators of someone who might be researching the topic. I don't know what you would accept as credible, but several researchers were mentioned in the article, one of whom has published here as well as at the conference mentioned in the article.

When the viral DNA/RNA inserted into a cell commands the cell to make more of it, if it inserts itself into the DNA to do so, nearby genes native to the cell can get copied along with the virus and "tag along for the ride", so to speak. Thus, when the new viruses infect a host cell of the same species (and sometimes different but similar species), they transmit the gene with them.

Cool. What I wonder then, is how quickly this process can unfold? I'm sure it depends on the conditions, but viruses and bacteria can multiply very quickly, so in an amenable environment it seems there could be quite a bit of transfer occurring.

 

[PsychoSarah]

Again, I was only looking for indicators of someone who might be researching the topic. I don't know what you would accept as credible, but several researchers were mentioned in the article, one of whom has published here as well as at the conference mentioned in the article.

I generally don't trust sources that don't have citations, though it is plenty possible that the article references works within its body. At best, not having the citations (or, links to the reference works) is a mark of laziness. At worst, it means there is no source material or the supposed source material portrays the topic in a way incompatible with the intent of the article.

Cool. What I wonder then, is how quickly this process can unfold? I'm sure it depends on the conditions, but viruses and bacteria can multiply very quickly, so in an amenable environment it seems there could be quite a bit of transfer occurring.

For bacteria, it happens pretty fast with all the varieties of horizontal gene transfer that apply to them. Not so much for eukaryotic organisms such as ourselves, since horizontal gene transfer has fewer mechanisms that apply, and the ones that do are far less fast than those of bacteria. In the case of the gene by virus transfer method, that the native gene gets dragged along for the ride is hardly a guarantee, and it happening once doesn't mean the viral offspring will do it every time.

 

[Loudmouth]

1) What is the success rate for absorbing DNA? Do the bacterial organisms absorb DNA from their hosts 100% of the time, 1%, 0.01%?

The article you linked to seems to focus on horizontal transfer between bacteria, not between the bacteria and its animal host. If I remember right, eukaryotic DNA is methylated which means it is difficult for bacteria to take up and use. Most of my experience is with transferring bacterial DNA to other bacteria.

A quick scan of the literature turned up this paper by Dr. Havarstein:

A predatory mechanism dramatically increases the efficiency of lateral gene transfer in Streptococcus pneumoniae and related commensal species

In this paper they had the attacking bacteria (S. pneumo) and the "prey" bacteria that carried an antibiotic resistance marker. They allowed the S. pneumo bacteria to kill and lyse the prey bacteria, and then counted how many of the S. pneumo bacteria were took up the DNA responsible for antibiotic resistance.

Using the data in table 2, they had 300 million attacking S. pneumo of which 200,000 became resistant (indicating transfer of that specific DNA). That would be 0.1%. Keep in mind that is in perfect lab conditions which may be quite different than conditions in the host.

3) Do the bacterial organisms appear to target specific regions of their host DNA, or is it random?

It appears that incorporation of the DNA from the environment into the bacterial genome requires homologous recombination. This means that there needs to be some sequence homology between the DNA taken up from the environment and the DNA found in the genome of the bacteria that grabbed the DNA.

The mechanism is pretty straightforward. Complementary bases (A--T, G--C) like to stick to one another through hydrogen bonds, so when you have a long string of DNA bases that match between two DNA strands they will stick to one another, and then be incorporated into the genome.

 

[Loudmouth]

Resha,

If you are interested in engineered systems used in the research lab I am familiar with the Clostron system. We used E. coli to harbor a plasmid designed to knockout a gene in a Clostridial species, and then used conjugation (i.e. bacterial sex) to transfer the plasmid from E. coli to the target bacteria.

ClosTron.com

If you have any questions, feel free to ask.

 

[Resha Caner]

If you are interested in engineered systems used in the research lab I am familiar with the Clostron system.

I noticed that most literature (such as DNA computing) is focused on deterministic results, for understandable reasons. I'm more interested in non-deterministic results, and that was a facet of the research I had proposed to the university I spoke with.

I generally don't trust sources that don't have citations, though it is plenty possible that the article references works within its body. At best, not having the citations (or, links to the reference works) is a mark of laziness. At worst, it means there is no source material or the supposed source material portrays the topic in a way incompatible with the intent of the article.

That's a reasonable caution, but the approach is a useful way for me to chase an idea. The search terms that come to my mind often don't match with the technical jargon used by biologists. So, my first hits are often pop science, and then I have to chase the clues to "translate" the idea/question into the proper format.

For bacteria, it happens pretty fast with all the varieties of horizontal gene transfer that apply to them. Not so much for eukaryotic organisms such as ourselves, since horizontal gene transfer has fewer mechanisms that apply, and the ones that do are far less fast than those of bacteria. In the case of the gene by virus transfer method, that the native gene gets dragged along for the ride is hardly a guarantee, and it happening once doesn't mean the viral offspring will do it every time.

Maybe a little clarification would help. Amongst all the combinations, the instance where a prokaryote picks up DNA from a eukaryote is the one that interests me (which I believe was the nature of the article in post #7). I'm not sure if the distinctions you're making covered that.

If I remember right, eukaryotic DNA is methylated which means it is difficult for bacteria to take up and use.

The article refers to a case where the prokaryote is well into decomposition. Maybe that makes a difference?

The two basic questions I'm asking may have gotten a little scattered, so I'll repeat. I'm asking about speed and extent. For example, could the bacteria pick up enough DNA from the mammoth to become a prokaryote? And how fast could that happen?

 

[Loudmouth]

The two basic questions I'm asking may have gotten a little scattered, so I'll repeat. I'm asking about speed and extent. For example, could the bacteria pick up enough DNA from the mammoth to become a prokaryote? And how fast could that happen?

Since the bacteria incorporate DNA through homologous recombination I doubt they would use much, if any, mammoth DNA. There needs to be sequence homology between the external DNA and the internal genome, and that doesn't exist to any real extent between the S. pneumo and mammoth genomes.

 

[Loudmouth]

I noticed that most literature (such as DNA computing) is focused on deterministic results, for understandable reasons. I'm more interested in non-deterministic results, and that was a facet of the research I had proposed to the university I spoke with.

Almost all of the tech and processes I am aware of in the field of DNA/RNA manipulation use the binding of complementary bases, which is a very deterministic process. If you want to detect DNA to DNA interactions then you are going to have to focus on either binding or extension of the molecule, both of which are going to be template driven and dependent on complementary bases.

I have no idea what the goal of your project is, but it sounds like you may be leaning towards an array of short DNA molecules. By having a large array of deterministic outcomes you may be able to discern between discrete processes, assuming that this is what you want to do in the first place. DNA/RNA arrays do exist, so this might interest you.

 

[Resha Caner]

Since the bacteria incorporate DNA through homologous recombination I doubt they would use much, if any, mammoth DNA. There needs to be sequence homology between the external DNA and the internal genome, and that doesn't exist to any real extent between the S. pneumo and mammoth genomes.

I thought HGT was considered a mechanism by which organisms can acquire new traits. That would seem to indicate a substantial amount of DNA transfer without sequence homology. Am I missing something? Are there 2 different mechanisms involved?

 

[Loudmouth]

I thought HGT was considered a mechanism by which organisms can acquire new traits. That would seem to indicate a substantial amount of DNA transfer without sequence homology.

In the case of S. pneumo, it does require sequence homology.

Some species take up DNA readily while others do not. For example, it is nearly impossible to transform (i.e. get external DNA into the inside of) Clostridial species.

You also have to understand that there are many different mechanisms. For example, genes can hitch a ride in phage genomes which are then inserted into the host genome through the usual process of phage integration. You can also have transfer of plasmids which are like little mini-chromosomes that stay separate from the rest of the genome. Then you can have very rare events where non-homologous DNA just happens to be in the right spot to get integrated into a genome through random processes.

On top of all of this, HGT just isn't as common as you think. It's not as if it is happening all of the time.

 

[Resha Caner]

In the case of S. pneumo, it does require sequence homology.

Some species take up DNA readily while others do not. For example, it is nearly impossible to transform (i.e. get external DNA into the inside of) Clostridial species.

OK. Got it.

You also have to understand that there are many different mechanisms. For example, genes can hitch a ride in phage genomes which are then inserted into the host genome through the usual process of phage integration. You can also have transfer of plasmids which are like little mini-chromosomes that stay separate from the rest of the genome. Then you can have very rare events where non-homologous DNA just happens to be in the right spot to get integrated into a genome through random processes.

Sure.

On top of all of this, HGT just isn't as common as you think. It's not as if it is happening all of the time.

I would assume there are conditions that would promote a particular mechanism.

 

[Loudmouth]

I would assume there are conditions that would promote a particular mechanism.

That would seem to be a safe assumption. Digging back through the memory banks I remember reading papers on the SOS response and how it increases recombination rates in starvation conditions. I would imagine that different pH, salt, and nutrient conditions can affect bacterial conjugation. DNA damage through starvation, mitomycin treatment, or UV exposure can also induce phage reproduction and lysis.

When you are talking about millions of species of bacteria and multiple mechanisms for HGT, you can imagine the amount of variations you can find.

 

[FrumiousBandersnatch]

... could the bacteria pick up enough DNA from the mammoth to become a prokaryote?

? Bacteria are prokaryotic.

 

[PsychoSarah]

? Bacteria are prokaryotic.

And mammoths are eukaryotic.
If he meant to ask if, by absorbing DNA of a eukaryote, could a bacteria become a eukaryote, then the answer to that question is no. The rare instances of a bacteria even incorporating eukaryotic DNA are in far too small amounts, and would not disrupt the signature ring shape of prokaryotic DNA into the linear DNA of a eukaryote.

 

[Resha Caner]

? Bacteria are prokaryotic.

Sorry. That was a typo. It should have read, "Could the bacteria pick up enough DNA from the mammoth to become a eukaryote?"

@PsychoSarah FYI, I'm male.