Despite eons of mingling inside our cells, gene networks we've inherited from primitive, singled-celled ancestors have stayed separate. Our cells remain chimeras, a hybrid fusion of unrelated creatures.

The genes date from an event 1.5 billion years ago, when two kinds of simple cells, neither having a nucleus or cellular membrane, shacked up and created an entirely new form of life: eukaryotes.

While the two distinct communities of genes work together to keep cell machinery ticking, they otherwise stay out of each other's hair, report biologists from the National University of Ireland.

"We humans, as part of the eukaryotes, we're still a community of two prokaryotes," said James McInerney, co-author of a study published in* Genome Biology and Evolution*, July 27. *

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While some scientists think prokaryotes evolved directly into eukaryotes, others think it required a merger, with two cells – one archaebacteria and one eubacteria – joining at some prehistoric point to make a cell capable of complex internal structures.

The merger led to an explosion of innovation. Suddenly cells could divide labor into ministructures, known as organelles, letting them specialize and grow larger. The extra biochemical whiz-bangery in eukaryotic cells makes lifeforms like orchids and dolphins possible.

"This idea is a hundred years old," said McInerney. "But we wanted to ask, 'If you have two types of organisms coming together to form a new kind of cell, do their metabolisms become completely blended together? What happens when genomes fuse?'"

To find out, McInerney and his colleague David Alvarez-Ponce surveyed the human genome and separated the genes into three groups based on taxonomic molecular signatures. One set contained genes inherited from our eubacterial ancestor, one from the archaebacterial ancestor and one held genes unique to eukaryotes. (Fingernail protein, for example, has no ancient doppelganger.)

'You would have thought someone would have noticed this, but nobody ever did.'Molecular tests showed that proteins coded by ancient parent cells still interact mostly with each other.

"They've found an imprint of this original symbiosis remaining after 1.5 billion years," said Bill Martin, an endosymbiosis researcher at Heinrich-Heine-Universität Düsseldorf, in Germany and editor of the journal publishing the study. "This is a brilliant discovery. You would have thought someone would have noticed this, but nobody ever did."

Beyond that, McInerney and Alvarez-Ponce found gene communities hold different functions. Archaebacterial genes are usually responsible for information processing, and appear to be especially important. They've accumulated fewer DNA mutations than eubacterial genes, suggesting that changes are more likely to have major consequences.

Eubacterial genes tended to be involved in biochemical processes. They were also more likely to be implicated in heritable human disease risk.

That more-important archaebacterial genes are found less frequently in disease might seem counterintuitive, but McInerney thinks the imbalance might exist because archaebacterial gene mutations often prevent organisms from developing at all.

Mutations to eubacterial biochemical process genes may cause problems, but organisms at least live long enough for disease to occur.

McInerney expects the study will cause a stir in the evolutionary biology community.

"When it comes to the origin of something big – the origin of sex, the origin of multicellularity, the origin of life and the origin of the eukaryotic cell – people get very argumentative," he said. "What this study does is copper-fasten the idea that the eukaryotic cell is genuinely a chimeric organism."

Image: GE Healthcare**/Flickr.

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Citation: "The human genome retains relics of its prokaryotic ancestry: human genes of archaebacterial and eubacterial origin exhibit remarkable differences." By David Alvarez-Ponce and James O. McInerney. Genome Biology and Evolution, July 27, 2011.