How horizontal gene transfer complicated the tree of life

All of life can be ordered into a tree, with branches separating and growing out as new species arise and become extinct, only the longest branches extending in the current day. It is an attractive image, promoted, of course, by Lamarck and Darwin, but it is not as simple as it appears.

As we know, genes are passed down from parents to their offspring, but there are some rare events where genes are passed between unrelated individuals. This phenomenon is called horizontal or lateral gene transfer. It is estimated that 5-6% of the bacterial genome is derived from horizontal transfer and that its role in multi-celled organisms is also being uncovered. It complicates our traditional idea of nicely ordered trees by adding lines between branches. It may seem like it may just be used for jaded scientists who study evolution but it has direct implications on humans, more particularly, for human health.

The tree of life. Image credits: Ernst Haeckel from the The Evolution of Man .

Ways genes can be transferred horizontally

There are three ways that genes can be passed between unrelated individuals; these are conjugation, transformation, and transduction.

(1) Conjugation passes genetic material via cell-to-cell contact, often through plasmids, which are circular units of DNA that are able to replicate on their own. The cells can inject these plasmids into other cells.

(2) Transformation involves bacteria incorporating DNA directly from their environment, such as from dead cells that have split open and released their genetic contents.

(3) Transduction occurs when a virus, in particular a bacteriophage, transfers DNA from one cell to another. Bacteriophages are unable to replicate on their own so they override the bacterial replication machinery in a host cell, making it replicate the virus instead until the cell is so full of virus particles that it ruptures. These new phages are then released into the environment to infect more hosts. Some phages alternate between infecting hosts and lysogeny, where they combine their genome with the bacterial chromosome and go inactive for multiple generations. When they take themselves out of the bacterial chromosome, they sometimes take some pieces of bacterial DNA with them.

How horizontal gene transfer can occur. Image credits: 2013MMG320B.

Consequences on…

Okay, so organisms can transfer genes to other organisms but how does that matter? Horizontal transfer has huge consequences, in particular, for the virulence of bacteria, helpful adaptations for other organisms, human cancers, and how we study evolution.

Bacterial resistance

Since bacteria can share and incorporate foreign DNA so easily, this process has played an important role in their evolution. Unfortunately for us, this makes them extremely adaptable and a ferocious opponent. One huge problem that humans are facing is the development of bacterial resistance to our antibiotics. The reason that antibiotic resistance can spread so easily is that one bacterium can evolve the resistance and then pass it on to unrelated bacteria through the previously mentioned mechanisms. It can also cause other adaptations that are good for bacteria but bad for humans, including evolving the ability to degrade compounds such as pesticides.

The bacteria in the right Petri dish has developed resistance to antibiotics. Image credits:
Dr Graham Beards.

Human health

Horizontal gene transfer is not just limited to single celled organisms. There has been even more evidence of this process in multicellular organisms as well. A recent study including 40 genomes from different types of animals found that they had genes transferred from bacteria and fungi, some relatively recently. These sequences may still be functionally within their new hosts. The results supported other studies that found that human genes, like FTO, the fat mass and obesity-associated gene, may have been horizontally transferred.

In some cases, horizontal gene transfer can cause human cancers. The human papillomavirus (HPV) can integrate itself into cervical cells and if they are not completed integrated, some proteins become unregulated causing the cells to proliferate unbounded, causing cancer. The hepatitis B virus behaves in a similar way for hepatocellular cancer. A researcher at the University of Georgia has found bacterial integrations in 36 genes in gastric samples with cancer. It is unclear though if it is a side effect or cause of cancer. In addition to cancer, horizontal gene transfer has helped out pathogens that invade humans. Bites from assassin bugs can infect humans with trypanosomal Chagas disease, which can insert its DNA directly into the human genome. The malaria pathogen has acquired some human DNA, which could help it to stay longer in the body.

The course of evolution

There are many cases of transferred genes that can be useful to their host and help the host to evolve to their environment. There are too many to go into detail here but I will highlight a few. The coffee berry borer beetle is the most notorious pest for coffee production. The gene that allows the pest to eat coffee berries is a mannanase gene that comes from bacteria. The invasive mamorated stink bug might also have a similar gene from bacteria which helps to cause major crop damage.

A bdelloid rotifer. Image credits: Danelle Vivier.

To our current knowledge, bdelloid rotifers are the animals with the highest amount of horizontal gene transfer; 8% of their genes come from bacteria. Not all genes horizontally transferred come from bacteria, hornworts gave the ferns a gene for surviving in dark forests about 180 millions years ago. An agrobacterium gave plants genes that causes cells to proliferate as roots and crown galls.

The study of evolution

The discovery of horizontal gene transfer has complicated the way that scientists figure out how related species are to each other. In the past, some relationships were shown based on the sequencing of a single gene. If two distantly related species have exchanged that gene, the phylogenetic tree will portray them as very closely related although most of their other genes and evolutionary history are very different. The most common gene for constructing phylogenetic relationships has been the 16S ribosomal RNA gene, as it is often conserved among closely related species. However, recent research has shown that this gene can also be horizontally transferred.

An illustration of horizontal gene transfer’s affect on the tree of life. Image credits: Barth F. Smets, Ph.D.

Now, it is best practice to use a wide range of different genes to infer phylogenetic relationships between species to avoid this problem. Bacterial genomes have been more sequenced than eukaryote genomes because they are smaller so there has been a bias. What we know about horizontal gene transfer and its prevalence will likely increase as genomic databases expand.

Horizontal gene transfer might have flipped what we know about evolution on its head, but it gives us new insight into how life is interconnected.

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