Horizontal gene transfer in eukaryotes

By Heiloi Yip

The conventional image of the evolution of life is often portrayed by the imagery of a tree with many diverging branches, with lineages dividing along the tree. As such, a lineage is only ever connected to a point where another nearby lineage has branched off. There are times, however, when two branches are connected laterally, even if the two branches sit very far apart from each other. Such lateral connections represent the exchange of genetic material between two unrelated lineages. Horizontal gene transfer (HGT) is the transfer of genetic material between two organisms, which can be either closely or very distantly related. This occurs when one organism acting as a ‘donor’ copies one or several of its own genes to a ‘recipient’ organism, thus potentially granting the ‘recipient’ new phenotypes. 

HGT is a very common process between bacteria, often seen in the form of an antibiotic resistant strain sharing the genes that confer said resistance to other bacteria. While the mechanism for HGT between bacteria is studied extensively, HGT involving eukaryote organisms is not well understood. There are many obstacles to successful gene transfer in eukaryotes. Because a eukaryote’s genetic material is enveloped behind a nuclear membrane along with the cell membrane, donated genes must pass two physical barriers before being successfully integrated into the genome. The problem is further complicated in complex multicellular organisms, where only the genes of the germline cell (i.e. sperm and egg) get passed onto the next generation. Therefore, a very specific set of cells are required to be involved in HGT for any phenotypic effect to occur. Furthermore, even if the genetic material is successfully integrated into the genome, there are no guarantees that it will still be functional.  Indeed, most HGT events end up as ‘junk’ DNA in the genome (Yoshida et al., 2019). 

Despite these odds, some genes from eukaryotic organisms have been proven to originate from distant lineages of organisms, sometimes resulting in major evolutionary consequences. For example, some lineages of beetles possess a group of enzymes that allow for the digestion of tough plant matter. Analysis of the enzymes’ genetic sequences demonstrates that they are homologous to similar enzymes found in bacteria. It is believed that an HGT event occurred between a gut bacterium and a primitive beetle, allowing the beetles to enter herbivory and rapidly diverge into multiple different species (McKenna et al., 2019). 

Consistent instances of HGT can be found in the exchange of genetic material between a eukaryotic cell and its symbiotic organelles. Genetic analysis into the genome of a plant cell, along with those of the mitochondria and chloroplasts taken from the same cell, has found pieces of plant DNA within the genomes of the mitochondria and chloroplasts, and vice versa. This find is significant because mitochondria and chloroplasts were believed to once have been individual organisms, as simple prokaryotes with independent genomes. At some point after an ancestral eukaryote ‘swallowed’ the early mitochondria and chloroplast, DNA must have been exchanged between the eukaryote nucleus and the symbionts, gradually altering all three genomes over the course of the eukaryote’s evolution. As such, it appears to be possible for eukaryotes to receive genes from prokaryotes, provided they are in very close proximity to each other (Neelapu et al., 2019).

It is established that HGT can occur frequently between symbiote and eukaryote, but there is potential for other kinds of prokaryotes to be involved. Wolbachia is a genus of gram-negative bacteria, living as intracellular parasites that infect insects and nematodes. Wolbachia possess special adaptations that seem to allow a much higher chance of successful HGT events with its eukaryotic hosts. Firstly, Wolbachia infects eukaryotic cells by living within the cell’s cytoplasm. Similarly to the endosymbionts, this puts Wolbachia’s genome in close proximity to that of its host’s, increasing the frequency of genes transferred between the two genomes. Secondly, Wolbachia tends to infect the reproductive organs of their host, meaning that Wolbachia regularly comes in contact with the host’s germline cells. Since any changes in the genome of germline cells are passed onto the next generation, HGT events can have impacts on the evolution of Wolbachia’s hosts (de Miguel, Zhu & Villa, 2019). 

Though technically not living organisms, viruses can also be agents of HGT. When a host cell is infected, newly formed viruses can accidentally pick up fragments of host DNA along with the replicated viral genome. As the virus emerges and infects a different host (sometimes distantly related), the ‘imported’ fragment has a chance to be integrated into a new genome. This process has been documented occurring between bacteria, but a similar mechanism for eukaryotes is yet to be discovered. Nonetheless, retroviruses may play a role in eukaryote HGT, as they infect eukaryotes and target the nucleus, integrating their genetic material into the host genome. In essence, the virus disguises itself as one of the host’s gene before its activation. Any ‘imported’ genes in the virus would also become integrated into the host genome, and the cell will carry these additional genes provided it survives the viral infection. In short, viruses can act as a medium for HGT between organisms that are physically too far apart for direct transfer of DNA (Yoshida et al., 2019).

Today, bioinformatics can reveal genetic sequences that are derived from HGT events, identifying segments of DNA that appear to be inserted from a separate group. Combined with the ability to sequence entire genomes of various organisms, newly discovered HGT events can reveal more details about an organism’s evolutionary history (Yoshida et al., 2019).

HGT has also been linked to the development of cancer, as foreign genes entering a cell (e.g. inserted by a retrovirus) could potentially trigger uncontrolled growth, resulting in the formation of a tumour. For example, it has been hypothesized that HGT between gut bacteria and the intestinal epithelial cells is a potential cause of gastrointestinal tumours. Perhaps, once the mechanisms underlying eukaryotic HGT is fully understood, a new method to treat a multitude of diseases can be developed, delivering vital genes to faulty cells in order to restore a variety of functionality (Abril, Lanzi & Notario, 2019). 

References:

Abril, A., Lanzi, P. and Notario, V., 2019. Implications of Lateral or Horizontal Gene Transfer from Bacteria to the Human Gastrointestinal System for Cancer Development and Treatment. Horizontal Gene Transfer, pp.377-397. DOI: 10.1007/978-3-030-21862-1_16

de Miguel, T., Zhu, O. and Villa, T., 2019. Horizontal Gene Transfer Between Wolbachia and Animals. Horizontal Gene Transfer, pp.227-234. DOI: 10.1007/978-3-030-21862-1_8

McKenna, D., Shin, S., Ahrens, D., Balke, M., Beza-Beza, C., Clarke, D., Donath, A., Escalona, H., Friedrich, F., Letsch, H., Liu, S., Maddison, D., Mayer, C., Misof, B., Murin, P., Niehuis, O., Peters, R., Podsiadlowski, L., Pohl, H., Scully, E., Yan, E., Zhou, X., Ślipiński, A. and Beutel, R. (2019). The evolution and genomic basis of beetle diversity. Proceedings of the National Academy of Sciences, 116(49), pp.24729-24737. DOI: 10.1073/pnas.1909655116

Neelapu, N., Mishra, M., Dutta, T. and Challa, S., 2019. Role of Horizontal Gene Transfer in Evolution of the Plant Genome. Horizontal Gene Transfer, pp.291-314. DOI: 10.1007/978-3-030-21862-1_12

Yoshida, Y., Nowell, R., Arakawa, K. and Blaxter, M., 2019. Horizontal Gene Transfer in Metazoa: Examples and Methods. Horizontal Gene Transfer, pp.203-226. DOI: 10.1007/978-3-030-21862-1_7

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