Not all of our genetic endowment has been passed down vertically, through ancestral lines. Some of it has been acquired horizontally, from “foreign” sources, such as bacteria, protists, and fungi. The degree to which animals and humans have acquired foreign genes is unclear. It is a matter of some controversy. Yet, according to scientists from the University of Cambridge, foreign genes may have been acquired in sufficient number to influence the course of our evolution.
The transfer of genes between organisms living in the same environment is known as horizontal gene transfer (HGT). It is well known in single-celled organisms, and it is thought to be an important process that explains how quickly bacteria evolve, for example, resistance to antibiotics. In multicellular organisms, however, few cases of HGT have been documented.
HGT is thought to play an important role in the evolution of some animals, including nematode worms, which have acquired genes from microorganisms and plants, and some beetles that gained bacterial genes to produce enzymes for digesting coffee berries. However, the idea that HGT occurs in more complex animals, such as humans, rather than them solely gaining genes directly from ancestors, has been widely debated and contested.
Hoping to clarify matters, the University of Cambridge scientists took advantage of the recent availability of a sufficient number of high-quality genomes and associated transcriptomes to carry out a detailed examination of HGT in 26 animal species (10 primates, 12 flies, and 4 nematodes) and a simplified analysis in a further 14 vertebrates. After carrying out genome-wide comparative and phylogenetic analyses, the scientists determined that HGT in animals typically gives rise to tens or hundreds of active foreign genes, largely concerned with metabolism.
These findings appeared March 13 in the journal Genome Biology, in an article entitled, “Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes.” This article confirmed that a number of genes, including the ABO blood group gene, had been acquired by vertebrates through HGT. The majority of the other genes were related to enzymes involved in metabolism.
For example, some of the genes that had been acquired by humans via horizontal transfer were shown to be involved in lipid metabolism, including the breakdown of fatty acids and the formation of glycolipids. Others were shown to be involved in immune responses, including the inflammatory response, immune cell signaling, and antimicrobial responses, while further gene categories include amino-acid metabolism, protein modification, and antioxidant activities.
The study’s lead author Alastair Crisp, D.Phil., said, “This is the first study to show how widely HGT occurs in animals, including humans, giving rise to tens or hundreds of active foreign genes. Surprisingly, far from being a rare occurrence, it appears that HGT has contributed to the evolution of many, perhaps all, animals and that the process is ongoing, meaning that we may need to re-evaluate how we think about evolution.”
In humans, the scientists confirmed 17 previously reported genes acquired from HGT, and identified 128 additional foreign genes in the human genome that have not previously been reported.
“HGT occurs at low, but appreciable, levels across all the animal species we examined; it has occurred over time and is still occurring; it mainly originates from bacteria and protists; and the genes concerned frequently code for enzyme activities,” wrote the authors of the Genome Biology article. “Interestingly, overall levels of HGT do not appear to be conspicuously different in vertebrates and invertebrates. This is surprising given the difference in complexity between the groups, but may be explained by the observed older HGT in primates, suggesting that the vertebrate HGT may have occurred at an earlier stage of vertebrate evolution.”
The authors say that their analysis probably underestimates the true extent of HGT in animals and that direct HGT between complex multicellular organisms is also plausible, and already known in some host-parasite relationships.
The study also has potential impacts on genome sequencing more generally. Genome projects frequently remove bacterial sequences from results on the assumption that they are contamination. While screening for contamination is necessary, the potential for bacterial sequences being a genuine part of an animal's genome originating from HGT should not be ignored, say the authors.