Horizontal Gene Transfer

Did you know that genetic material can be transferred between distantly-related organisms? This process is called horizontal gene transfer. We will discuss horizontal gene transfer: its definition, types, manifestation in bacteria, importance, and detection methods.

What is the Definition of Horizontal Gene Transfer?

Horizontal gene transfer -also known as lateral gene transfer- is a general term for the non-sexual exchange of genetic material among organisms, even between distantly-related species. It is distinct from the vertical transfer, in which genetic material passes on from parent to offspring.

This distinction can be better understood through Figure 1, a phylogenetic tree that shows how genetic material moves vertically (through reproduction) and horizontally (through horizontal gene transfer).

Figure 1. This diagram illustrates how genetic material moves vertically through reproduction and horizontally through horizontal gene transfer across the different domains of life.

Three Types of Horizontal Gene Transfer

Horizontal gene transfer occurs through transformation, conjugation, and transduction. These processes are illustrated in Figure 2 below. We will discuss each of these types in the following section.

Figure 2. This diagram shows how the 3 types of horizontal gene transfer occur in bacteria.

Transformation

Transformation is one of the most common mechanisms of horizontal gene transfer among bacteria. Transformation happens when a recipient competent cell takes up the extracellular naked DNA from the environment or DNA from a dead donor bacterium.

Transformation involves homologous recombination, the exchange of genetic material between single-stranded or double-stranded nucleic acids that have extensive regions of similar base sequences. Donor and recipient cells are usually of the same bacterial species.

Conjugation

Another mechanism of horizontal gene transfer in bacteria is conjugation. Conjugation is the most common mechanism of horizontal gene transfer from a donor bacterial species to a different recipient species. Bacterial conjugation was first discovered in E. coli, and it relies on cell-to-cell contact. The direct contact of cells with each other is important for bacterial conjugation and distinguishes it from other mechanisms of horizontal gene transfer.

In bacterial conjugation, the donor cell would pull the recipient cell using a structure called a sex pilus. Sex pilus is a tube-like appendage that allows cell-to-cell contact, and it protects the transfer of DNA plasmid from the donor to the recipient cell. Once they are in contact with each other, DNA is pushed out of the donor cell and transported to the recipient cell.

Transduction

Transduction involves the transfer of DNA fragments through a viral vector called a bacteriophage. A bacteriophage is a virus that can infect bacteria. Bacteriophage, the transducing particle, would infect a bacterium and then inject its DNA into the bacteria. After injection, the DNA from the virus can hijack the bacterium and use it as a host to make more of the DNA. Unlike conjugation, transduction does not require physical contact between the donor cell and the receiver cell.

Transduction can happen by a lytic or lysogenic cycle. In the lytic cycle, the bacteriophage takes over the bacterial cell's replication, transcription, and translation machinery to direct it to make new viral particles. Once there are viral particles, it is released into the environment via the lysis of the host.

On the other hand, in a lysogenic cycle, the bacteriophage chromosome is inserted as a prophage into the bacterial chromosome. This prophage can remain dormant in the bacteria, but the prophage can be excised from the bacterial chromosome and initiates the lytic cycle if the bacteria is induced.

Example of Horizontal Gene Transfer in Bacteria

Bacteria are versatile organisms that can take up foreign DNA, replicate it, and pass it down to future generations. They can respond to selective pressure and adapt to their new environment via different mechanisms. They are also able to adapt because they can acquire new genetic traits. These new genetic traits are acquired either through mutation or modification of gene faction from horizontal gene transfer. We will briefly discuss these two processes in the following section.

Mutation

Mutation occurs very slowly in nature; mutation rates vary from 10-6 to 10-9 per nucleotide per bacterial generation. Other times, mutation can happen faster, such as if a bacteria population is under a lot of stress from the environment. However, most mutations in bacteria are lethal and lead to death.

Horizontal gene transfer

Through horizontal gene transfer, bacteria can adapt rapidly by acquiring DNA from another bacterium in a single transfer. Horizontal gene transfer is involved in bacterial genome evolution, DNA damage prevention, virulence, antibiotic resistance, and overall survival in different environmental stresses.

A critical aspect of horizontal gene transfer in bacteria is the exchange of antibiotic resistance genes. Exchange in antibiotic resistance genes leads to evolution and plays a role in developing multi-drug resistant bacteria that are pathologically relevant to humans. Most resistance genes rapidly evolve and spread among different human pathogens.

Detecting Horizontal Gene Transfer

The ability to detect horizontal gene transfer is important in the research and medical field. In health sciences, horizontal gene transfer has a significant role in the evolution of new pathogens, especially in promoting antibiotic resistance in bacterial species, which usually leads to multi-drug resistant pathogens. Genes that confer antibiotic resistance are horizontally transferred, for example, from a sensitive Staphylococcus aureus bacteria, resulting in a methicillin-resistant strain.

The two most commonly used methods in detecting horizontal gene transfer are the phylogeny-based approach and the composition-based approach, which utilize different bioinformatics tools.

Phylogeny-based Approach

In a phylogeny-based approach, a large set of gene copies of the gene being investigated is compared and contrasted to the phylogeny of their originating species. If there are differences between the investigated gene and the phylogeny, it is reconciled by introducing horizontal gene transfer. This approach allows us to identify ancient horizontal gene transfer events in a genome, but it only works under strict restrictions.

This approach relies on multiple sequence alignment (MSA) and the reliability and accuracy of existing phylogenetic species trees. The gene transferred should also originate from a relatively distant donor from the recipient cell, so divergence can be detected.

Composition-based Approach

In a composition-based approach, the genome is compared and contrasted based on its properties. Limitations of this approach stem from similar compositional patterns of different species. Also, the length of the gene transferred from donor to recipient may be too small to be detected.