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

March 12, 2015
genes
This image shows the coding region in a segment of eukaryotic DNA. Credit: National Human Genome Research Institute

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 (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 , including nematode worms which have acquired genes from microorganisms and plants, and some beetles that gained 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 , 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 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 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.

Explore further: Primitive microbes stole bacterial genes on a surprising scale

More information: 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

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7 comments

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tadchem
5 / 5 (2) Mar 12, 2015
One conclusion of this work is that all primates evolved from GMOs.
JVK
1 / 5 (5) Mar 12, 2015
See also:
http://news.scien...rganisms "It makes it clearer than ever that there has been a history, throughout evolution, of gene transfer between organisms."

This can be placed into the context of other works that link viral microRNAs and nutrient-dependent microRNAs from ecological variation to ecological adaptations manifested in RNA-mediated cell type differentiation via amino acid substitutions that differentiate all cell types in all individuals of all species.

See for a historical representation of top-down causation: http://journals.p....1003035

See, for examples across other species: Nutrient-dependent/pheromone-controlled adaptive evolution: a model. http://www.ncbi.n...24693353

It has been obvious for more than 15 years that the RNA-mediated molecular mechanisms are conserved. See: http://www.gregbe...ture.cfm
JVK
1 / 5 (5) Mar 12, 2015
See also: Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses http://elifescien...abstract

https://www.youtu...NcMR_-RU
https://www.youtu...youtu.be
Captain Stumpy
3.7 / 5 (6) Mar 13, 2015
See, for examples across other species: Nutrient-dependent/pheromone-controlled adaptive evolution: a model. http://www.ncbi.n...24693353
2jimmie k
EXCEPT that this "model" is totally DEBUNKED in the following two links: http://www.socioa...ew/24367
http://rspb.royal...full.pdf

so why should we trust you on biology when almost EVERY biologist alive says you are a crackpot?
like here: http://freethough...s-place/

PLUS: EVER TIME you try to interpret a link to a study with your own perspective, you are proven WRONG when the author actually replies

shall i start linking all those posts too?

stop trying to interpret the science from your RELIGIOUS PERSPECTIVE
http://www.ploson...tion=PDF
JVK
1 / 5 (4) Mar 13, 2015
Journal article conclusion: "Although observed rates of acquisition of horizontally transferred genes in eukaryotes are generally lower than in prokaryotes, it appears that, far from being a rare occurrence, HGT has contributed to the evolution of many, perhaps all, animals and that the process is ongoing in most lineages. Between tens and hundreds of foreign genes are expressed in all the animals we surveyed, including humans. The majority of these genes are concerned with metabolism, suggesting that HGT contributes to biochemical diversification during animal evolution." http://genomebiol.../16/1/50

See also: http://www.ncbi.n...3960071/
"Among different bacterial species existing in similar environments, DNA uptake (Palchevskiy & Finkel, 2009) appears to have epigenetically 'fed' interspecies methylation and speciation via conjugation.... This indicates that reproduction began with with an active nutrient uptake mechanism..."
JVK
1 / 5 (4) Mar 13, 2015
Re: "...reproduction began with with an active nutrient uptake mechanism..." The metabolism of nutrients to species-specific pheromones controls the physiology of reproduction in all other species.

The ability to recognize a pattern of biophysically constrained protein folding that is nutrient-dependent and RNA-directed via DNA methylation and amino acid substitution that stabilize the RNA-mediated chemistry of protein folding is required to link top-down causation via what is currently known about molecular epigenetics in species from microbes to man.

However, as you can see in the discussion of "The search for human pheromones" http://phys.org/n...nes.html there are many biologically uniformed science idiots who are not capable of pattern recognition. Some appear to think that proof of top-down causation must be provided in example from every species on this planet before what's known can be compared to evolutionary theory.
Vietvet
4 / 5 (4) Mar 13, 2015
JVK=Creationist=science idiot

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