Opening the book…
Many gene transfer mechanisms are regulated by social and/or ecological interactions between organisms.[411]The mechanisms involved can be complex; one could easily imagine an entire course focused on this topic. We introduce only the broad features of these systems. Also, we want to be clear about the various mechanisms of DNA uptake. When an organism dies its DNA can be eaten by others as a source of energy, carbon, nitrogen, and phosphorus. When eaten the information in the DNA, the result of mutation and selection, is lost.[412] Alternatively, the released DNA molecule can be integrated into another organism’s genome, resulting in the possible acquisition of whatever information was present in the sequence. This information might be useful, harmful, or irrelevant to the organism that acquires it. The study of these natural DNA import, as distinct from conjugation-mediated transfer systems has identified some of the specific molecular machines involved. Some organisms use a system that preferentially imports DNA molecules derived from organisms of the same or closely related type. You can probably imagine how they might do this – one way could be that they have receptor systems that recognize species-specific “DNA uptake sequences.” The various mechanisms of horizontal gene transfer, unsuspected until relatively recently, have had profound influences on evolutionary dynamics, particularly within microbial communities, where they appear to be more common than among eukaryotes. The result is that, in many cases, an organism in such a population does not have to “invent” all of its own genes, it can adopt (import) genes generated by evolutionary mechanisms in other organisms in other environments for other purposes. So the question is, what advantages might such information uptake systems convey, and (on the darker side), what dangers do they make possible?
Transformation
There are well established methods, used in genetic engineering, to enhance the ability of bacteria to take up DNA from their environment.[413] Here wemfocus on natural transformation. Natural transformation is an active (energy-requiring) process that involves a number of components, encoded by genes that can be expressed or not depending upon environmental conditions. Consider a type of bacteria that can import DNA from its environment. If the density of bacteria is low, there will be little DNA to import, and it may not be worth the energetic expense associated with expressing the genes and synthesizing and assembling the proteins involved in the DNA uptake and 
integration machinery. Bacteria use quorum sensing systems (considered earlier) to monitor cell density and to control the expression of genes involved in the synthesis of the DNA uptake system. When present in a crowded environment, the quorum sensing system can turn on the expression of the genes involved in DNA uptake system.
Here we outline the process in one type of bacteria but functionally similar mechanisms are used in other bacterial and archaeal species. Double-stranded DNA binds to the cell’s surface through a variety of DNA receptor proteins. In some cases these receptors bind specific DNA sequences, in others they bind DNA generically, that is, any DNA sequence. As shown, Gram negative bacteria have two lipid membranes, an outer one and an inner (plasma) membrane, with a periplasmic space, between them. In an ATP-hydrolysis coupled reaction, DNA bound to the exterior surface of the bacterium is moved, through a protein pore across the outer membrane and into the periplasmic space, where it is passed to the DNA channel protein (→). Here one strand of the DNA is degraded by a nuclease while the other moves intact through the channel into the cytoplasm of the cell in a 5’ to 3’ direction (similar to the one-strand transfer seen in bacterial conjugation). Once inside the cell, the DNA associates with single-stranded DNA binding proteins and, by homologous recombination, can be inserted into the host genome (or degraded, depending on the system).[414] While the molecular details of this and functionally similar processes are best addressed elsewhere, what is key is that transformation enables a cell to take up foreign DNA and to add the imported DNA sequences to its own genome.
Virus moving genes: transduction
The final form of horizontal gene transfer that we will consider involves bacterial viruses. The structure and behavior of viruses is a complex topic, the details of which are largely beyond us here, but it is not unreasonable to consider viruses as nucleic acid transport machines. Viruses are dependent for their replication on the infected host cell, they have no active metabolic processes. They are not alive in any meaningful sense of the word. That said, they are infectious, they can spread through a population. Viruses cannot be killed, because they are not alive, but they can be inactivated by various treatments.
Viruses contain a nucleic acid genome and a protein-based transport and delivery system. We consider (briefly) a typical bacterial virus, known as a bacteriophage or bacteria eater. The T4
bacteriophage T4, looks complex and it is (→), other viruses are somewhat simpler. The T4 phage, short for bacteriophage, has a ~169,000 base pair double-stranded DNA genome that encodes 289 polypeptides, almost as many as a minimal cell (see above).[415] The assembled virus has an icosahedral protein head that contains a DNA molecule attached to a tail assembly that recognizes and binds to target cells. Once a suitable host cell is found, based on tail binding to cell surface molecules, the tail domain attaches to the cell's surface and contracts, like a syringe, punching a hole through the bacterial cell’s external wall and plasma membrane. The DNA emerges from the bacteriophage and enters the cytoplasm, infecting the cell. Genes within the phage genome are expressed, leading to the replication of the phage genome and the fragmentation of the host cell’s DNA.[416] The phage DNA encodes the proteins used to build and assemble new phage. DNA is packed into these heads by a protein-based DNA pump (↓) driven by an ATP hydrolysis reaction complex.[417] In the course of packaging viral DNA, the system will, occasionally, make a mistake and package a fragment of the host cell’s DNA. When such a phage particle infects another cell, it can inject that cell with a DNA fragment derived from the previous host. The mis-packaged DNA may 
not contain all of the genes the virus needs to make a new virus or to kill the host. If this is the case, the host cell may have to be co-infected by a wild type virus for the mutant virus to replicate. The DNA transferred by the virus to the host can be inserted into the host cell's genome, with the end result being similar to that discussed previously for transformation and conjugation. DNA from one organism is delivered to another, horizontally rather than vertically.
Because the horizontal movement of DNA via toxic viruses is common in the microbial world, a number of defense mechanisms have evolved to control it.[418] These include restriction endonuclease / DNA modification systems used widely for genetic engineering, and the CRISPR-Cas9 system that enables cells to recognize and destroy foreign (viral) DNAs. These systems, evolved as part of the prokaryotic immune systems, together with various plasmids form the tools used in modern molecular biology and genetic engineering methods. They illustrate how studying apparently arcane aspects of the biological world, bacterial viral defense mechanisms, can have dramatic impacts on modern technological, medical, and economic systems.
Questions to answer:
- What is an asexual clone? How would you recognize it.
- What is the effect of an amorphic allele / mutation on the behavior of a prokaryotic clone.
- What are some possible (evolutionary) advantages to the ability to take up and integrate, as opposed to simply eat foreign DNA?
- Why might the “source” of foreign DNA matter?
- Present a plausible model that would identify host from foreign DNA
- Propose a model by which a “selfish” plasmid might evolve into a virus.
- How can co-infection of a cell with wild type virus "rescue" a virus that has lost some of its essential genes?
- How might inserting a piece of DNA into a bacterium's genome be harmful
Questions to ponder:
- Describe a mechanism by which a prokaryotic organism might protect itself from invading viruses?
- How is it that "punching a hole" in a membrane (during DNA uptake or phage infection) does not kill the cell?
- How does vertical differ from horizontal inheritance?
Possible extension:
- Introduce and consider the role of the lysogenic / lytic switch in bacteriophage / bacterial interactions.
- Extend discussion to mobile genetic elements
Short Chapter Summary
- Bacteria/archaea exchange genes via transformation, transduction, and conjugation—evolution on fast-forward.
- HGT spreads innovations (e.g., antibiotic resistance); “sex” without meiosis still reshapes populations.
References
[411] DNA uptake during bacterial transformation: http://www.ncbi.nlm.nih.gov/pubmed/15083159
[412] This is of course why genes are rarely if ever transferred from food to the organism doing the eating.
[413] Making Calcium Competent (bacterial) Cells: http://mcb.berkeley.edu/labs/krantz/protocols/calcium_comp_cells.pdf
[414] Bacterial transformation: distribution, shared mechanisms and divergent control & Natural competence and the evolution of DNA uptake specificity
[415] http://en.wikipedia.org/wiki/Bacteriophage_T4
[416] An infected bacterial cell can protect is neighbors, often its clonal relatives, if it can kill itself before the virus can replicate. This is an example of a simple altruistic behavior.
[418] see The phage-host arms-race: Shaping the evolution of microbes
This page titled 11.2: Other naturally occurring horizontal gene transfer mechanisms was last modified on Thu, 08 Jan 2026 23:38:55 GMT and is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by Michael W. Klymkowsky and Melanie M. Cooper.
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