Some genes 'foreign' in origin and not from our ancestors

March 12, 2015

Many animals, including humans, acquired essential 'foreign' genes from microorganisms co-habiting their environment in ancient times, according to research published in the open access journal Genome Biology. The study challenges conventional views that animal evolution relies solely on genes passed down through ancestral lines, suggesting that, at least in some lineages, the process is still ongoing.

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 thought to be an important process that explains how quickly bacteria evolve, for example, resistance to antibiotics.

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.

Lead author Alastair Crisp from the University of Cambridge, UK, said: "This is the first study to show how widely horizontal gene transfer (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."

The researchers studied the genomes of 12 species of Drosophila or fruit fly, four species of nematode worm, and 10 species of primate, including humans. They calculated how well each of their genes aligns to similar genes in other species to estimate how likely they were to be foreign in origin. By comparing with other groups of species, they were able to estimate how long ago the genes were likely to have been acquired.

A number of genes, including the ABO blood group gene, were confirmed as having been acquired by vertebrates through HGT. The majority of the other genes were related to enzymes involved in metabolism.

In humans, they confirmed 17 previously-reported genes acquired from HGT, and identified 128 additional foreign genes in the human genome that have not previously been reported.

Some of those genes were involved in lipid metabolism, including the breakdown of fatty acids and the formation of glycolipids. Others were involved in immune responses, including the inflammatory response, immune cell signalling, and antimicrobial responses, while further gene categories include amino-acid metabolism, protein modification and antioxidant activities.

The team were able to identify the likely class of organisms the transferred genes came from. Bacteria and protists, another class of microorganisms, were the most common donors in all species studied. They also identified HGT from viruses, which was responsible for up to 50 more foreign genes in primates.

Some genes were identified as having originated from fungi. This explains why some previous studies, which only focused on bacteria as the source of HGT, originally rejected the idea that these genes were 'foreign' in origin.

The majority of HGT in primates was found to be ancient, occurring sometime between the common ancestor of Chordata and the common ancestor of the primates.

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.
-end-
Media Contact

Joel Winston
Media Officer
BioMed Central
T: +44 (0)20 3192 2081
E: Joel.Winston@biomedcentral.com

Notes to editor:

1. Research article

Alastair Crisp, Chiara Boschetti, Malcolm Perry, Alan Tunnacliffe and Gos Micklem

Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes

Genome Biology 2015

DOI: 10.1186/s13059-015-0607-3

After embargo, article available at journal website here: http://dx.doi.org/10.1186/s13059-015-0607-3

For an embargoed copy of the article, please contact Joel.Winston@biomedcentral.com

2. Genome Biology serves the biological research community as an international forum for the dissemination, discussion and critical review of information about all areas of biology informed by genomic research. Key objectives are to provide a guide to the rapidly developing resources and technology in genomics and its impact on biological research, to publish large datasets and extensive results that are not readily accommodated in traditional journals, and to help establish new standards and nomenclature for post-genomic biology.

3. BioMed Central is an STM (Science, Technology and Medicine) publisher which has pioneered the open access publishing model. All peer-reviewed research articles published by BioMed Central are made immediately and freely accessible online, and are licensed to allow redistribution and reuse. BioMed Central is part of Springer Science+Business Media, a leading global publisher in the STM sector. http://www.biomedcentral.com

BioMed Central

Related Bacteria Articles from Brightsurf:

Siblings can also differ from one another in bacteria
A research team from the University of Tübingen and the German Center for Infection Research (DZIF) is investigating how pathogens influence the immune response of their host with genetic variation.

How bacteria fertilize soya
Soya and clover have their very own fertiliser factories in their roots, where bacteria manufacture ammonium, which is crucial for plant growth.

Bacteria might help other bacteria to tolerate antibiotics better
A new paper by the Dynamical Systems Biology lab at UPF shows that the response by bacteria to antibiotics may depend on other species of bacteria they live with, in such a way that some bacteria may make others more tolerant to antibiotics.

Two-faced bacteria
The gut microbiome, which is a collection of numerous beneficial bacteria species, is key to our overall well-being and good health.

Microcensus in bacteria
Bacillus subtilis can determine proportions of different groups within a mixed population.

Right beneath the skin we all have the same bacteria
In the dermis skin layer, the same bacteria are found across age and gender.

Bacteria must be 'stressed out' to divide
Bacterial cell division is controlled by both enzymatic activity and mechanical forces, which work together to control its timing and location, a new study from EPFL finds.

How bees live with bacteria
More than 90 percent of all bee species are not organized in colonies, but fight their way through life alone.

The bacteria building your baby
Australian researchers have laid to rest a longstanding controversy: is the womb sterile?

Hopping bacteria
Scientists have long known that key models of bacterial movement in real-world conditions are flawed.

Read More: Bacteria News and Bacteria Current Events
Brightsurf.com is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to Amazon.com.