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[Update 13-Jan - more info] Evolution of complexity recreated using 'molecular time travel'

[Update 13-Jan] article from arstechnica added

Our cells are filled with complexes that can contain dozens of proteins, all with precise interactions that ensure the complex comes together and functions in a consistent manner. These complexes, which can contain dozens of individual proteins, often have activities that mimic those of human-produced equipment, and have earned the nickname "molecular machines" accordingly.

If a molecular machine requires so many precisely positioned parts to function, how could it possibly evolve? That question has been part of a populist attack on evolution but, contrary to its proponents, scientists have a number of ideas about the evolution of this machinery. It's just that those ideas can be very hard to test, since we can't go back in time and look at the predecessors to today's machines.

Advances in DNA sequencing, however, have allowed us to calculate what the earlier proteins must have looked like. And scientists have now started to engineer DNA sequences that "resurrect" these long dead proteins, and examine how they function. In the latest work of this sort, a team has resurrected parts of an ancient molecular machine, and shown how some of its specialized protein components evolved.

The complex in question is an ATP-driven proton pump. It burns ATP, the cell's power source, and uses that energy to send protons across a membrane. In this case, the pump controls the pH of a compartment within the cell, which is necessary for survival under certain conditions. But its very similar to a far more important complex, the one that runs in reverse and harvests differences in proton concentrations to make ATP, and thus provide power to the cell.
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Scientists find that small, high-probability mutations can produce complex system

Much of what living cells do is carried out by "molecular machines" – physical complexes of specialized proteins working together to carry out some biological function. How the minute steps of evolution produced these constructions has long puzzled scientists, and provided a favorite target for creationists.

In a study published early online on Sunday, January 8, in Nature, a team of scientists from the University of Chicago and the University of Oregon demonstrate how just a few small, high-probability mutations increased the complexity of a molecular machine more than 800 million years ago. By biochemically resurrecting ancient genes and testing their functions in modern organisms, the researchers showed that a new component was incorporated into the machine due to selective losses of function rather than the sudden appearance of new capabilities.

"Our strategy was to use 'molecular time travel' to reconstruct and experimentally characterize all the proteins in this molecular machine just before and after it increased in complexity," said the study's senior author Joe Thornton, PhD, professor of human genetics and evolution & ecology at the University of Chicago, professor of biology at the University of Oregon, and an Early Career Scientist of the Howard Hughes Medical Institute.

"By reconstructing the machine's components as they existed in the deep past," Thornton said, "we were able to establish exactly how each protein's function changed over time and identify the specific genetic mutations that caused the machine to become more elaborate."

The study – a collaboration of Thornton's molecular evolution laboratory with the biochemistry research group of the UO's Tom Stevens, professor of chemistry and member of the Institute of Molecular Biology – focused on a molecular complex called the V-ATPase proton pump, which helps maintain the proper acidity of compartments within the cell.

One of the pump's major components is a ring that transports hydrogen ions across membranes. In most species, the ring is made up of a total of six copies of two different proteins, but in fungi a third type of protein has been incorporated into the complex.

To understand how the ring increased in complexity, Thornton and his colleagues "resurrected" the ancestral versions of the ring proteins just before and just after the third subunit was incorporated. To do this, the researchers used a large cluster of computers to analyze the gene sequences of 139 modern-day ring proteins, tracing evolution backwards through time along the Tree of Life to identify the most likely ancestral sequences. They then used biochemical methods to synthesize those ancient genes and express them in modern yeast cells.

Thornton's research group has helped to pioneer this molecular time-travel approach for single genes; this is the first time it has been applied to all the components in a molecular machine.

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TAGGED: EVOLUTION, GENETICS, SCIENCE


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