A massive analysis of almost every bacterial genome sequenced to date suggests a new shape for the tree of life.

One of its core branches appears to be a union of two other branches. Descendants of that line became the energy centers of plant and animal cells.

In other words, the results of this distant union between microorganisms "allowed us to walk on the Earth," said James Lake, a University of California at Los Angeles cell biologist and author of the analysis. "It's responsible for the oxygen in the atmosphere, and brought in the organelles that made plants grow and let us breathe air."

The details of early cellular evolution are murky, with few fossils having remained intact for the billions of years since self-replicating chemicals assumed cellular form. But at a general level, scientists know that the earliest organisms were single-celled, nucleus-lacking creatures called prokaryotes.

These are broken down into five groups: bacteria, archaea, clostridia, actinobacteria and so-called gram-negative bacteria. To most people, prokaryotes are just a bunch of microscopic bugs, but to microbiologists they're as richly varied as the animal kingdom.

Scientists think the first eukaryotes — single-celled creatures with nuclei and complex internal structures, from which the entire plant and animal kingdom descended — evolved from prokaryotes, with some prokaryotes absorbed wholesale into these new and complicated organisms.

The best-known examples of this absorption are mitochondria and chloroplasts, the structures that generate energy in animal and plant cells. Both belong to the gram-negative class, as do cyanobacteria, which several billion years ago probably transmuted Earth's early atmosphere from a toxic soup to oxygen-rich air through photosynthesis.

According to Lake, the origin of this gram-negative group is not singular. Instead it appears to have been produced through a fusion of actinobacteria and clostridium. Were mammals derived from a union of insect and amphibian, the story-of-life rearrangement would be comparably profound.

"If these results can be confirmed and extended, they would undoubtedly have a major impact on our ideas about both prokaryotic and eukaryotic evolution," said Michael Gray, a Dalhousie University cell biologist best-known for identifying the bacterial origins of mitochondria. Gray was not involved in the research.

Lake's hypothesis, published Wednesday in Nature, is based on pattern analyses run on the genome sequences of more than 3,000 types of bacteria. For three years, he refined algorithms that teased out relationships between the different genes, then proposed different taxonomies to explain them.

Most importantly, he assumed that genes wouldn't necessarily flow in one direction, as they do in the animal kingdom. In bacteria, genes are swapped back and forth so easily that some scientists think the concept of species doesn't apply to them.

"People have always assumed that evolution works in a treelike manner. What we said was, let's analyze things in a way that doesn't assume the tree, and see what happens," said Lake.

Out of more than a million possible taxonomic arrangements, the one that best fit the data identified gram-negative prokaryotes as a descendant of some long-ago combination between members of the actinobacteria and clostridia groups.

It's impossible to test this against a fossil record, but it would explain why gram-negative prokaryotes and clostridia are both able to photosynthesize, a phenomenon that Gray called "heretofore puzzling."

"We've known about the gram-negative bacteria for three scientific generations. We've been staring at them for a hundred years, and we never realized how they came about or what made them so different," said Lake. "Without them, we wouldn't have eukaryotes as we do today."

According to Lake, the union likely took the form of endosymbiosis, in which one of the prokaryotes literally swallowed the other, and the two grew together. Gray called this interpretation of the data "problematic": It would have required one genome to cross a cell membrane to join the other. "I know of no such mechanism that would allow" this, said Gray.

But to Gray, the unlikelihood of an endosymbiotic union implies an as-yet-unknown process by which prokaryotes can fuse their entire genomes. That possibility "hasn't been widely considered within the evolutionary community," he said.

A decade ago, investigating such questions wouldn't even have been possible, said Lake. "We needed to have the mathematics and genomics to pull all this out of the sequences," he said.

See Also:

Citation: "Evidence for an early prokaryotic endosymbiosis." By James A. Lake. Nature, Vol. 460, No. 7258, August 20, 2009.

Images: 1. CRP-Sante 2. Nature

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