The Relaxosome: The Shuttlebus of Bacterial DNA
Bacteria are some of the simplest and most primitive organisms in existence. They also happen to be quite adept when it comes to sharing genetic information between each other.
Also, I like interesting and quirky biological terms that seem like they should be more popular, and that have not been talked about in a public way at length. Hence the curious titular subject: Relaxosome.
Note: I’m thankful to live in the modern day and age when all this information is freely available and composable, thanks to the efforts of countless others who came before me. All relevant links to primary and secondary sources have been posted on the term, and for any that sources I have missed citing, I will work to update this to include those references.
Disclaimer: None of the literature contained in this article is medical advice or to be taken as medical advice. This article is for informational purposes and potentially subject to errors which I’m constantly working to correct. Consult a physician if you have a medical issue.
Bacterial Gene Sharing
Why does any living thing share or duplicate its genes?
Well if the Selfish Gene Theory is to be believed, it’s because the organism is just the host, or rather the instrument of the DNA, which is actually “life” that is“trying to survive”. Depending on what you believe, the answer may be more spiritual than that.
Either way, life cannot propagate without propagation of the genetic material. Part of this survival is not only persisting the core material, but also increasing “genetic diversity” in order to evolve and survive changes to the environment.
While larger more complex organisms like human beings have only one natural method of transferring DNA to their offspring (reproduction), and no method of transferring DNA to each other to confer genetic diversity, bacteria have 3 major methods of doing this in addition to sexual reproduction.
- Sexual/Asexual Reproduction — the most common method increasing the genetic diversity of a bacterial population is through the standard process of an organism duplicating itself asexually (parthenogenesis), or sexually. Asexual reproduction doesn’t actually increase genetic diversity directly per-say, while sexual reproduction does by having the child organisms have a mixture of the parent’s DNA. This is called vertical gene transfer because genes are mixed, duplicated and transferred through generations of bacteria, altering the children, but not altering the parent.
- Bacterial Transduction — A method where viral replication is the main means by which bacteria transfer DNA to other bacteria. In this case the host bacteria of the carrier virus is destroyed after having its genome hijacked by a virus called a bacteriophage. The good thing is that the bacteria that are replicated by the virus have their DNA mixed with the DNA of a previous host bacterium, and this more diverse DNA is transferred to yet another bacterium.
- Bacterial Transformation — The process by which bacteria uptake freely floating DNA in the extracellular space which happens to contain enhancements to the bacterial DNA that can help improve its survivability.
- Bacterial Conjugation — Probably the most interesting process, in my opinion, of so called horizontal gene transfer. This is where a bacterium combines with another bacteria through a bridge structure called a pilus, to transfer some of its genetic information to another bacterium. There are no children produced: One bacteria simply confers genetic diversity to another bacteria — like a halfway sexual reproduction, without the reproduction part.
Bacterial Conjugation and Genetic Engineering
Let’s talk about bacterial conjugation a little more. Many bacterial species, particularly ones that are known for sharing genetic information have 2 sets of DNA:
- The Primary bacterial chromosome, which is free floating in the cytoplasmic space of the bacteria contains the bacteria’s primary genetic information, which is used to create the proteins and enzymes used to conduct its primary life processes. This contains the bulk of the genetic code, and can be quite massive and tangled in a relatively unorganized mess.
- Bacteria also have a small, well organized circular piece of DNA called a plasmid, which is much smaller than the primary bacterial chromosome, but which typically contains genes for “useful functions” of the bacteria, e.g. the ability to produce Beta Lactamase enzyme, which confers penicillin resistance to other bacteria. The plasmid is usually broken off from the larger bacterial chromosome to make replication of the particular genes it codes for much easier, as it’s far less tangled, and replication enzymes like DNA polymerase have a much easier time reading it.
The plasmid containing a sharable trait that the bacterium wants to pass to its “bretheren” is called an F-Factor or fertility factor, and a bacteria containing said fertility factor is said to be F+. If the bacteria don’t contain a plasmid that encodes a particular trait, then the bacteria is said to F-.
F+ bacteria, through the use of a tubular structure called the pilus have the ability to literally shuttle the a copy of the plasmid DNA through from one the donor bacteria to the receipt, and have it recombine with the host bacterium’s primary bacterial chromosome. This shuttle process is super interesting in that not only does it give us an understanding by which bacteria naturally share resistances to our drugs, it also provides a mechanism that genetic engineers can take advantage of to introduce new traits to host bacteria.
Let’s say for example, we want a bacteria to glow orange through adding a bioluminescence factor. We could introduce a plasmid into a bacterium turning it into an F+ bacterium for glowing orange. Next the bacterium will conjugate with a non-glowing F- bacteria, and turn it into another glowing F+ bacteria. One can imagine the “glowing trait” flowing through a population exponentially as more F- bacteria become F+ bacteria and help spread the glowing train more and more quickly.
The Relaxosome and Transfer/Replication of The Plasmid
Finally we get the topic of this article, the so called the Relaxosome.
Recall I mentioned that the plasmid was easy to duplicate and pass on to a host bacteria. The relaxasome is enzyme/protien complex which allows this fascinating process to occur.
By the way, if you are a microbiologist, you know about the genome of-course. But you should also be prepared to encounter many “-asomes”.
It’s just a biology thing.
First a super high level refresher: Most people know about DNA replication and the Central Dogma in Eukaryotes. The eukaryotic chromosome is a super-condensed collection strands of genetic material wrapped around proteins known as histones. During replication, the chromosome is unwound through a microbiologically complex process during mitotic cell division and replicated through the use of an enzyme called DNA Polymerase 3. Though we usually start to learn about this process in high school, this is done through a highly complex sequence of steps that takes many years of study to fully grasp, and is still an ongoing area of research.
Bacterial DNA replication is simpler since the bacterial chromosome isn’t nearly as complexly organized as the eukaryotic chromosome. We won’t go into the replication process of the larger bacterial chromosome, but rather we will focus on plasmid replication. The plasmid DNA, also has an asynchronous replication cycle that follows the so called “rolling circle process”.
The plasmid DNA exists, as almost all primary DNA does, in a well known double helix form in its least coiled state. In DNA replication this is done through a the use of an enzyme called Rep A, and the action of enzymes called Helicases, starting at a sub sequence of DNA called the origin of replication — or oriA.
Transfer of the plasmid from one bacteria to another requires that the strands are separated and unwound as well, but this process is done through an enzyme known as Relaxase. Relaxase is transferred to a site on the plasmid DNA known as the “origin of transfer” — or oriT.
The Relaxase literally pulls the DNA strands apart by breaking complementary base pairs. This occurs simultaneously as SSBs, or single stranded binding proteins hold the separated strands in place and also prevent it from degrading due to cytoplasmic instability. Remember the DNA is in a Helix for a reason — the helix provides environmental stability for the DNA molecule.
Transfer to the New Bacteria
The Relaxase at this point is still bound to the transfer-DNA strand. The relaxase is brought by a shuttle protein to the mouth of the pilus, also known as an exporter. Through a complex active transport system, the exporter, once loaded with the transfer-DNA pumps the relaxase and DNA through the exporter into the receipt cell.
Once in the recipient cell, the Relaxase then begins to wind the DNA back into a single helix form. How it does this is chemically extremely complex, as there is no guiding strand helping to mold the DNA onto — but I will for this article spare you the detail. Suffice to say, the Relaxase enzyme, for being a part of the so-called Relaxosome, is actually quite a type-A molecular machine.
Once the relaxase creates the helical circle, it unbinds from the DNA and joins the ends together, similarly to how the enzyme called DNA ligase joines fragments of DNA together during translation and other biological processes.
All the while that this is happening, plasmid replication is happening both in the single stranded DNA of the host cell via the action of DNA Polymerase 3, to turn it back into a double stranded molecule, and in the recipient cell, to ensure that the new plasmid is also stable. This processes occurs blazingly fast, and due to the error correcting capability of DNA polymerase, is highly mutation resistant.
Conclusion
The relaxosome is quite an important complex used by bacteria to pass traits from one bacteria to another. For those interested in synthetic biology, the relaxosome is one of the primary proteins used in facilitating so called bacteriological computation — the principle of horizontal gene transfer via bacterial conjugation being the prime driver of the computational mechanism.
Hope you enjoyed this introduction to the Relaxasome! See you next time!
